Gene loci information

Transcript annotation

  • This transcript has been annotated as Cubilin-like protein.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_4 g16259 g16259.t1 isoform g16259.t1 8885580 8891313
chr_4 g16259 g16259.t1 exon g16259.t1.exon1 8885580 8885797
chr_4 g16259 g16259.t1 cds g16259.t1.CDS1 8885580 8885797
chr_4 g16259 g16259.t1 exon g16259.t1.exon2 8886622 8887335
chr_4 g16259 g16259.t1 cds g16259.t1.CDS2 8886622 8887335
chr_4 g16259 g16259.t1 exon g16259.t1.exon3 8887437 8887593
chr_4 g16259 g16259.t1 cds g16259.t1.CDS3 8887437 8887593
chr_4 g16259 g16259.t1 exon g16259.t1.exon4 8887646 8888190
chr_4 g16259 g16259.t1 cds g16259.t1.CDS4 8887646 8888190
chr_4 g16259 g16259.t1 exon g16259.t1.exon5 8888484 8888655
chr_4 g16259 g16259.t1 cds g16259.t1.CDS5 8888484 8888655
chr_4 g16259 g16259.t1 exon g16259.t1.exon6 8888757 8889390
chr_4 g16259 g16259.t1 cds g16259.t1.CDS6 8888757 8889390
chr_4 g16259 g16259.t1 exon g16259.t1.exon7 8889525 8889650
chr_4 g16259 g16259.t1 cds g16259.t1.CDS7 8889525 8889650
chr_4 g16259 g16259.t1 exon g16259.t1.exon8 8889843 8890115
chr_4 g16259 g16259.t1 cds g16259.t1.CDS8 8889843 8890115
chr_4 g16259 g16259.t1 exon g16259.t1.exon9 8890200 8890775
chr_4 g16259 g16259.t1 cds g16259.t1.CDS9 8890200 8890775
chr_4 g16259 g16259.t1 exon g16259.t1.exon10 8891234 8891313
chr_4 g16259 g16259.t1 cds g16259.t1.CDS10 8891234 8891313
chr_4 g16259 g16259.t1 TSS g16259.t1 NA NA
chr_4 g16259 g16259.t1 TTS g16259.t1 NA NA

Sequences

>g16259.t1 Gene=g16259 Length=3495
ATGAAGTTGTGGAATTTTCTGATACTTTTAGTATCACTTAATAAAATTAAGAAAATTTCA
TCAGAACTTTATGATGATCAACCAAAAATTCTCGTCAACGATGGAAATTTAATTTTTGAA
TCAGCAAATTCCAAAGATATTTCTATAAAACTAAAAGGAAATTCTCGATTTTTAGTCAAT
AATCAAGATATTTTGTCACTCACAAATGTCACAAGAAATGACAAAACTTCGCAGTCACTT
CCATCATCAGATGCTACAAGTGTGCTCAATCAAATTCAAACATTCAAAGAAATTATTCGA
ACACAATCGCTAAGACTAAATGCAATTGAATACGACATAAATCATAATCAAAATGACACA
AATGGAACTGCATTAAATGATCGACAAAAATTCAATAGAATTAATCGAAGAATTAACAAT
CTTGAGCAAAGGTTAGCAAATTTAACAGAAAGATTGACAAAAGATCATTGTAAAAGTTAT
CCATGTCAAAATGGTGGAACTTGTTTCAATTTATACGACACATATCGATGTGAATGTAGA
GAAAATTATGAAGGACCACAATGTACTCTTGATGTTAATGAATGCGCAAGATATGCTGGA
ACTGATTTAGGTTGTCAAAATGGAGCTACTTGTATAAATACTGTTGGATCTTATGAATGC
ATTTGCCCAGAACACTGGACTGGCATTCATTGCAACCGTAGAAAAGTCGATTGTCTTTCA
GTACCACAATCTGAAATTTGTGGTCAAGGAATTTGTGTCCATGACAATAATAAAGATGGA
TATTCTTGCATTTGTAATCAAGGATGGAAAAAAGACAACAACAGTCGAGCTTGTACGCAA
GATGTTGATGAATGTCAAGAAATGAGACCTCATTGTTCTGTTGATCCTCCTGTGCTTTGT
GTTAATACACCTGGGTCTTTTGTTTGTGGTCCTTGTCCTGCTGGTTATCGTGGAAATGGT
TACTTCTGTAGAGACATTGATGAATGTGAAGTCAATAACGGAGGTTGTAGTATATCACCG
AAAGTTGAATGTTTAAATACTTATGGATCTTTCCGTTGTGGTCAATGTCCTCTTGGTTAT
GAAGGTGATGGAAGAGTTTGCATTCCACGTCAATCAAATACAGCCAATCAATGTGCAGAC
AGCAGTATTTGTAACTCTAATGCAATTTGTGTTCAATATCCAAATTCACCACCATCGTGT
ACATGCAAATTTGGTTTCACTGGCAACGGATTTGGTGATAATGGTTGTGTTCCTATGGCA
CCTGATCCATGCGTGGCACTTTTTTGTCGTAATGGAGGAACTTGCATTCGAAATGGAACT
CATCCTTATTGCAGTTGTCCACCAGGCACAAGTCCACCATTATGTGATAGAACTAGAAAT
GGTTGTGATCCAAATCCTTGTCGCAATGGAGGAAATTGCACAACTATGAGATTTGGTTTT
GGTTTTCGATGCACATGCCCTCGTGGATTTATTGGTGTTCGATGTGAAAATCAACAGTCA
ACATGTGGAGGCGTATTAAGTACTGAAAATGGAACTCTGCGATATCCAACTGATCCAACA
GCGACAACTTATCAACATAATTCGAGATGTGCATGGCTTATTAGAACAAACATTACAAAA
GTATTAAATATCACTTTCACATCATTTAATATTGAATTCAGTAATGAATGTCGATATGAT
TGGCTTCAAATCCACGACGGACGCTCAGCTGCATCACATATAATTGGTAGATTTTGTGGT
TCATCATTACCTAAAGGTGGCAACATAATTTCAACTCATAATCAACTTTATTTATGGTTT
AGATCAGACAATAGCACAGCTCATGATGGATTCGAATTGAAATGGGAATCAATTGATCCG
GTTTGTGGTGGTGAAAGCAACATAACAACACACGGAACAATTTCATCACCTGGTTCACCT
GGAAATTATCCAATAAACAGCGACTGTGAATGGATTTTGTTTGCTCCACCAGGGAAAAGG
ATTCAATTTTTATTCTACACTTTGATGATCGAAACTCATCCAACATGTGATTTTGATTTT
CTTGAAATTCACAGCGGTGATAGCACAGCGTCACCAAGTTTAGGAAAATTCTGCAATTCG
ACAGTTCCACCACCACTTTTGACACCTGGAAATGTTGCAACAATTCATTTTCATTCTGAT
GGTGACTCAACTGATGCCGGATTTCAAATTGCTTATTCAGTTATTGAAGGAATTCCAGGA
TGTGGTGGAATATATACGGCAGCTAAAGGTGACATTTCTTCACCAATGGATATTAATGAT
GGAACTTATAAACATAACTTATTATGTGATTATGTCATAAGAATGCCAACTGACACAAGA
ATTAGAATTGAATTTAAGAAATTTGGACTTGAAGAAAGTTCAACTTGTAAATTTGATGCA
GTTGAGATTTACGAAGGATCAGAAGACAGTGATGCATTAATTGGACGCTATTGTGGTTCA
ATAATGCCACCAATCATTACATCACAAACAAACATTGTTACTATCAAATTTATCACAGAT
TGGTCAACTAGTGACATTGGATTTCAACTTCAGTATCAATTAATTTGCGGTGGAATTTTC
ACATCAGAAACAGGAATAATTTCAAGTCCGAATTATCCAAATAATTATGATTCAGATAGA
TTATGTGAATATGACATAGTTGCACCACAAGGAAAAGTTATTGTTTTAAATGTTCTTGAT
TTTGATATTGAACAACATTCAATATGTGAATTTGATTATCTTCATGTTTATGATGGTGCA
ATTGCTGATAGTTCGACAAGTCTTGGAAGATTTTGTGGTGAAAATAAACCAGGAATTTTA
ACATCAACTTTCAATCAAATGCATATTGAATTTGCTACTGATGCTTCTGTTTTTGGTCGT
GGTTTTCAAGCAAATTACACTTTTGTTGATATAAAATGTGGTGGATTAATTAGAGATCAA
AAAGAATTAGTAAAACCGCCAATGGATGAAGATGACAATGGTGTTTATGAAGCAAATTCA
ATTTGTAAATGGCTTGTTGTTGCACCTAAAGGTTTTGTAATTCAAATGAATGTTTTGAAT
TTTGAATTGGAACATGATTCAGTTTGTAAATATGATTATTTAAAAATTTACAACAATGGA
AGTGGAAATGGCGAACAAATTGGACCATTTTGTGGAACAAATATTCCTAGAGTAATTACG
ACCAGTGATAATATTGCTACAATTGTTTTTGTTTCTGATTCTTCAACTGCAAAAGATGGC
TTTACAATTGGGTTCAATTTCATTGATGCTTCAAAATCATCAAGCAATCGATCACCAAAA
TATAAAAGAAAAAAAAGTTGTCCCATTCCAGTCATTAAAAGCGGCAATTCAACAATTGAA
GTTTTAAGACTGGTGTTATTTGCCATAATTGAAAAAAGACACAAAGAACAATTGATGAAA
CTGAAGACGCAATTTGCGAAGAAAAATGGCCAAAAAATTTCATTTAAAATTTTAGACATT
CTGAAATTAAATTGA

>g16259.t1 Gene=g16259 Length=1164
MKLWNFLILLVSLNKIKKISSELYDDQPKILVNDGNLIFESANSKDISIKLKGNSRFLVN
NQDILSLTNVTRNDKTSQSLPSSDATSVLNQIQTFKEIIRTQSLRLNAIEYDINHNQNDT
NGTALNDRQKFNRINRRINNLEQRLANLTERLTKDHCKSYPCQNGGTCFNLYDTYRCECR
ENYEGPQCTLDVNECARYAGTDLGCQNGATCINTVGSYECICPEHWTGIHCNRRKVDCLS
VPQSEICGQGICVHDNNKDGYSCICNQGWKKDNNSRACTQDVDECQEMRPHCSVDPPVLC
VNTPGSFVCGPCPAGYRGNGYFCRDIDECEVNNGGCSISPKVECLNTYGSFRCGQCPLGY
EGDGRVCIPRQSNTANQCADSSICNSNAICVQYPNSPPSCTCKFGFTGNGFGDNGCVPMA
PDPCVALFCRNGGTCIRNGTHPYCSCPPGTSPPLCDRTRNGCDPNPCRNGGNCTTMRFGF
GFRCTCPRGFIGVRCENQQSTCGGVLSTENGTLRYPTDPTATTYQHNSRCAWLIRTNITK
VLNITFTSFNIEFSNECRYDWLQIHDGRSAASHIIGRFCGSSLPKGGNIISTHNQLYLWF
RSDNSTAHDGFELKWESIDPVCGGESNITTHGTISSPGSPGNYPINSDCEWILFAPPGKR
IQFLFYTLMIETHPTCDFDFLEIHSGDSTASPSLGKFCNSTVPPPLLTPGNVATIHFHSD
GDSTDAGFQIAYSVIEGIPGCGGIYTAAKGDISSPMDINDGTYKHNLLCDYVIRMPTDTR
IRIEFKKFGLEESSTCKFDAVEIYEGSEDSDALIGRYCGSIMPPIITSQTNIVTIKFITD
WSTSDIGFQLQYQLICGGIFTSETGIISSPNYPNNYDSDRLCEYDIVAPQGKVIVLNVLD
FDIEQHSICEFDYLHVYDGAIADSSTSLGRFCGENKPGILTSTFNQMHIEFATDASVFGR
GFQANYTFVDIKCGGLIRDQKELVKPPMDEDDNGVYEANSICKWLVVAPKGFVIQMNVLN
FELEHDSVCKYDYLKIYNNGSGNGEQIGPFCGTNIPRVITTSDNIATIVFVSDSSTAKDG
FTIGFNFIDASKSSSNRSPKYKRKKSCPIPVIKSGNSTIEVLRLVLFAIIEKRHKEQLMK
LKTQFAKKNGQKISFKILDILKLN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
54 g16259.t1 CDD cd00054 EGF_CA 155 189 2.70669E-7
53 g16259.t1 CDD cd00054 EGF_CA 191 231 6.74971E-10
57 g16259.t1 CDD cd00054 EGF_CA 281 318 8.4599E-4
56 g16259.t1 CDD cd00054 EGF_CA 325 363 8.21355E-4
55 g16259.t1 CDD cd00054 EGF_CA 463 496 1.08117E-4
48 g16259.t1 CDD cd00041 CUB 502 617 1.01578E-29
52 g16259.t1 CDD cd00041 CUB 622 734 1.01724E-37
50 g16259.t1 CDD cd00041 CUB 741 853 2.99623E-31
49 g16259.t1 CDD cd00041 CUB 856 968 2.79027E-37
51 g16259.t1 CDD cd00041 CUB 996 1087 5.36702E-26
42 g16259.t1 Coils Coil Coil 124 158 -
35 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 115 192 5.8E-12
31 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 193 234 4.7E-12
34 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 290 328 1.8E-10
32 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 329 367 2.5E-9
33 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 369 413 9.6E-6
36 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 414 459 3.8E-5
30 g16259.t1 Gene3D G3DSA:2.10.25.10 Laminin 460 502 1.6E-9
40 g16259.t1 Gene3D G3DSA:2.60.120.290 - 503 618 5.8E-31
41 g16259.t1 Gene3D G3DSA:2.60.120.290 - 619 735 5.8E-34
39 g16259.t1 Gene3D G3DSA:2.60.120.290 - 736 854 7.9E-31
37 g16259.t1 Gene3D G3DSA:2.60.120.290 - 855 969 5.4E-37
38 g16259.t1 Gene3D G3DSA:2.60.120.290 - 970 1087 5.5E-25
13 g16259.t1 PANTHER PTHR45656:SF11 CUBILIN 108 755 1.7E-191
17 g16259.t1 PANTHER PTHR45656 PROTEIN CBR-CLEC-78 108 755 1.7E-191
14 g16259.t1 PANTHER PTHR45656:SF11 CUBILIN 762 850 1.7E-191
18 g16259.t1 PANTHER PTHR45656 PROTEIN CBR-CLEC-78 762 850 1.7E-191
12 g16259.t1 PANTHER PTHR45656:SF11 CUBILIN 846 1007 1.7E-191
16 g16259.t1 PANTHER PTHR45656 PROTEIN CBR-CLEC-78 846 1007 1.7E-191
11 g16259.t1 PANTHER PTHR45656:SF11 CUBILIN 995 1092 1.7E-191
15 g16259.t1 PANTHER PTHR45656 PROTEIN CBR-CLEC-78 995 1092 1.7E-191
1 g16259.t1 Pfam PF00008 EGF-like domain 157 186 3.7E-7
2 g16259.t1 Pfam PF00008 EGF-like domain 203 230 5.9E-8
4 g16259.t1 Pfam PF07645 Calcium-binding EGF domain 281 317 1.9E-7
5 g16259.t1 Pfam PF07645 Calcium-binding EGF domain 325 367 2.2E-6
3 g16259.t1 Pfam PF12661 Human growth factor-like EGF 429 449 0.055
6 g16259.t1 Pfam PF00431 CUB domain 502 614 6.2E-23
10 g16259.t1 Pfam PF00431 CUB domain 622 732 2.2E-23
8 g16259.t1 Pfam PF00431 CUB domain 741 852 3.0E-25
7 g16259.t1 Pfam PF00431 CUB domain 856 966 1.4E-30
9 g16259.t1 Pfam PF00431 CUB domain 995 1085 2.1E-22
44 g16259.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
45 g16259.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
46 g16259.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 13 -
47 g16259.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 21 -
43 g16259.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 1164 -
84 g16259.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 168 179 -
80 g16259.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 177 188 -
83 g16259.t1 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 191 220 -
85 g16259.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 211 222 -
81 g16259.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 220 231 -
82 g16259.t1 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 325 353 -
78 g16259.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 484 495 -
79 g16259.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 484 495 -
91 g16259.t1 ProSiteProfiles PS50026 EGF-like domain profile. 153 189 19.642
95 g16259.t1 ProSiteProfiles PS50026 EGF-like domain profile. 191 232 18.896
92 g16259.t1 ProSiteProfiles PS50026 EGF-like domain profile. 374 412 11.615
94 g16259.t1 ProSiteProfiles PS50026 EGF-like domain profile. 420 456 15.406
93 g16259.t1 ProSiteProfiles PS50026 EGF-like domain profile. 458 496 19.807
87 g16259.t1 ProSiteProfiles PS01180 CUB domain profile. 502 618 24.41
88 g16259.t1 ProSiteProfiles PS01180 CUB domain profile. 622 735 25.455
86 g16259.t1 ProSiteProfiles PS01180 CUB domain profile. 741 855 23.379
89 g16259.t1 ProSiteProfiles PS01180 CUB domain profile. 856 969 29.072
90 g16259.t1 ProSiteProfiles PS01180 CUB domain profile. 973 1088 21.528
60 g16259.t1 SMART SM00179 egfca_6 153 189 3.9E-4
72 g16259.t1 SMART SM00181 egf_5 156 189 1.7E-4
64 g16259.t1 SMART SM00179 egfca_6 191 232 5.6E-11
77 g16259.t1 SMART SM00181 egf_5 194 232 2.2E-6
59 g16259.t1 SMART SM00179 egfca_6 235 279 0.14
75 g16259.t1 SMART SM00181 egf_5 237 279 0.017
63 g16259.t1 SMART SM00179 egfca_6 281 324 3.7E-4
74 g16259.t1 SMART SM00181 egf_5 284 324 9.5
61 g16259.t1 SMART SM00179 egfca_6 325 368 3.4E-5
70 g16259.t1 SMART SM00181 egf_5 328 368 8.5
71 g16259.t1 SMART SM00181 egf_5 377 417 3.0
58 g16259.t1 SMART SM00179 egfca_6 422 456 0.65
73 g16259.t1 SMART SM00181 egf_5 423 456 0.016
62 g16259.t1 SMART SM00179 egfca_6 458 496 0.73
76 g16259.t1 SMART SM00181 egf_5 461 496 1.3E-5
66 g16259.t1 SMART SM00042 CUB_2 502 618 2.0E-31
67 g16259.t1 SMART SM00042 CUB_2 622 735 2.5E-35
65 g16259.t1 SMART SM00042 CUB_2 741 855 6.4E-36
68 g16259.t1 SMART SM00042 CUB_2 856 969 2.8E-43
69 g16259.t1 SMART SM00042 CUB_2 973 1088 1.4E-26
26 g16259.t1 SUPERFAMILY SSF57196 EGF/Laminin 155 196 1.05E-10
20 g16259.t1 SUPERFAMILY SSF57184 Growth factor receptor domain 195 329 9.26E-9
19 g16259.t1 SUPERFAMILY SSF57184 Growth factor receptor domain 282 424 1.46E-5
28 g16259.t1 SUPERFAMILY SSF57196 EGF/Laminin 419 457 9.49E-5
27 g16259.t1 SUPERFAMILY SSF57196 EGF/Laminin 460 498 7.57E-8
22 g16259.t1 SUPERFAMILY SSF49854 Spermadhesin, CUB domain 499 623 3.93E-30
25 g16259.t1 SUPERFAMILY SSF49854 Spermadhesin, CUB domain 630 735 1.83E-33
21 g16259.t1 SUPERFAMILY SSF49854 Spermadhesin, CUB domain 738 857 4.97E-31
24 g16259.t1 SUPERFAMILY SSF49854 Spermadhesin, CUB domain 856 969 1.7E-37
23 g16259.t1 SUPERFAMILY SSF49854 Spermadhesin, CUB domain 971 1087 4.06E-25
29 g16259.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0038024 cargo receptor activity MF
GO:0005509 calcium ion binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values