General information for g11445.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Collagen alpha-1(XVIII) chain.
Parent gene
- The parent gene g11445 is located on chr_1: 16305287..16305802 (- strand)
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_1 | g11445 | g11445.t2 | TTS | g11445.t2 | 16300976 | 16300976 |
| chr_1 | g11445 | g11445.t2 | isoform | g11445.t2 | 16301514 | 16305802 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon1 | 16301514 | 16301650 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS1 | 16301514 | 16301650 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon2 | 16301716 | 16301787 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS2 | 16301716 | 16301787 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon3 | 16301869 | 16301927 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS3 | 16301869 | 16301927 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon4 | 16301993 | 16302181 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS4 | 16301993 | 16302181 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon5 | 16302243 | 16302373 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS5 | 16302243 | 16302373 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon6 | 16302432 | 16302473 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS6 | 16302432 | 16302473 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon7 | 16302530 | 16302661 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS7 | 16302530 | 16302661 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon8 | 16302729 | 16302821 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS8 | 16302729 | 16302821 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon9 | 16302875 | 16302948 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS9 | 16302875 | 16302948 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon10 | 16303009 | 16303038 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS10 | 16303009 | 16303038 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon11 | 16303096 | 16303129 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS11 | 16303096 | 16303129 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon12 | 16303223 | 16303309 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS12 | 16303223 | 16303309 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon13 | 16303377 | 16303453 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS13 | 16303377 | 16303453 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon14 | 16303596 | 16303623 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS14 | 16303596 | 16303623 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon15 | 16303702 | 16303727 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS15 | 16303702 | 16303727 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon16 | 16303783 | 16303840 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS16 | 16303783 | 16303840 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon17 | 16304241 | 16304263 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS17 | 16304241 | 16304263 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon18 | 16304324 | 16304432 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS18 | 16304324 | 16304432 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon19 | 16304509 | 16304583 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS19 | 16304509 | 16304583 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon20 | 16304680 | 16304756 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS20 | 16304680 | 16304756 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon21 | 16304823 | 16304833 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS21 | 16304823 | 16304833 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon22 | 16304995 | 16305034 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS22 | 16304995 | 16305034 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon23 | 16305114 | 16305143 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS23 | 16305114 | 16305143 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon24 | 16305210 | 16305288 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS24 | 16305210 | 16305288 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon25 | 16305584 | 16305727 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS25 | 16305584 | 16305727 |
| chr_1 | g11445 | g11445.t2 | exon | g11445.t2.exon26 | 16305794 | 16305802 |
| chr_1 | g11445 | g11445.t2 | cds | g11445.t2.CDS26 | 16305794 | 16305802 |
| chr_1 | g11445 | g11445.t2 | TSS | g11445.t2 | 16306518 | 16306518 |
Sequences
>g11445.t2 Gene=g11445 Length=1866
ATGGCTATGGTTATATCAAGTAGAGCAAAAGGGATGATTGGCGCATTTATATCATTGATA
CTTTTATCAACTGTTCTTGTAACTGCATCGACAAAAGGCTGGTGGTTTGGTTTAAATAAA
AATAATGGTGAACATGTTGCTGCTCGAATACAGGCAAACAGTGACTCAGATTTTAATGAT
TATAGTAACGAAAATGAAAGTCCAGTTTTACAGGCTCCACCAGATTTTAAGAATTATGGT
GGATACAGAAAGGGTGAAAAAGGTGAGAAGGGAGCTAGAGGAATTCCAGGCGATTCAATC
AGAGGGCCACCTGGACCTCCAGGTCCAAAAGGAGAATGTCAAATAGTTAATTTTAATAAT
AATACCAACAGTTACAATAATAATTTCAAACAGACGGAACAAAAATTAGCACCAGTTTGT
GCATGTAATTACGACAATATTATTGATATTCTTCACAATGAATCGGTAATTCAAATTCTA
CGAGGCCCTCAAGGCCCTCCGGGATTAACGGGAGCTCCCGGTCAAAAAGGGGAAATGGGC
GAAAGAGGAGCAGATGGTATTGATGGAATTCCAGGATTGCCAGGGACACCAGGAGAGGAA
TCAATGATGGGAAGCATTCGTGGCAAGGATTCACGAGGAGAAAAAGGCGATAAAGGCGAT
ATGGGTATGAAAGGAATGAAGGGAGAAGGTGGAGCAAAAGGAGAAAAAGGAGCATGTATA
ACAGTTCCAGAAATACAGACTAACAATTGCGGTTGTCCATTCAATGATACATACAAAGGA
ATAAAGGGAGATAAAGGGCTTAGAGGAAAACGTGGAAAAACTGGCAGTCAAGGAGAAAAA
GGACAGAAAGGAGATAGTGGGTCATCAGTGGGGCCAAAAGGTGACAAAGGAGAGCGAGGT
CAACCAGGTCTGCCAGGACCACCTTTTAGTGGCTTTGATGACTCAATGAATTATCAACGA
TCAGGAATCGGCACAATAATCACATTTCAAAATACTGACACAATGATAAAACAATCATCT
ACATATCCTGTAGGTTCAATTTGTTATGTTATAGATGAGGAAGCTCTGTTAGTGAAAGTT
TCAAAAGGATGGCAATACATTGCTCTTGGCACATTATTACCATTCACAACTCCTTATGTA
ACCACTTCACCAATGTCTCCAACTTCCTACATGGACCTTCAAGCTTCAAATTTGCTCAAC
AGTAACAGTATTTTAAAGTCTCCTGAGAGCTATACATTTACAACACCTCCAGAATATGAA
ACATGGAATCCAAAAATGTTAAGATTGATTGCATTGAATGAACCATACTCTGGTAATTTA
CAAGGTTTACGAAACGCTGATTTAAATTGTCATCGACAAGCAAGACGATCTGGATTGATG
GGTAACTTTAGAGCTTTCTTATCAACTAGAATTCAGAACTTGGATTCTCTAATAAAACCC
GAAGACAGAGAATTGCCAATAACAAACTTGCGTGGGGATGTGCTTTTTAATTCATTCAAC
GCTATTTTCAATAATAATGCTCAAGGAATCTTTCTGTCATCCAATTCACCGCGAATTATT
AGCTTCAGTGGCAAAAATGTGATGAATGACAATACTTGGCCTCATAAAATTGTTTGGCAT
GGCGCACGTGCGGATTCAATAGACACAAATTGTGAAGGTTGGCATAGCAATTTTCAAGAT
AAGGTTGGTTTAGGGAGCAGTCTGTTAGGAAATAAGTTACTTGCTCAAGAAATGTATAGT
TGTCAGCAAAAGAATATTGTTCTATGCATTGAAGTGTTATCGCATAGTAGCAGTGGTGAT
ATTGCAAATCGTCGAAAGCGTGAGATGATGCAGAGTAATGACGATACATACGACAACGAA
AAATGA
>g11445.t2 Gene=g11445 Length=621
MAMVISSRAKGMIGAFISLILLSTVLVTASTKGWWFGLNKNNGEHVAARIQANSDSDFND
YSNENESPVLQAPPDFKNYGGYRKGEKGEKGARGIPGDSIRGPPGPPGPKGECQIVNFNN
NTNSYNNNFKQTEQKLAPVCACNYDNIIDILHNESVIQILRGPQGPPGLTGAPGQKGEMG
ERGADGIDGIPGLPGTPGEESMMGSIRGKDSRGEKGDKGDMGMKGMKGEGGAKGEKGACI
TVPEIQTNNCGCPFNDTYKGIKGDKGLRGKRGKTGSQGEKGQKGDSGSSVGPKGDKGERG
QPGLPGPPFSGFDDSMNYQRSGIGTIITFQNTDTMIKQSSTYPVGSICYVIDEEALLVKV
SKGWQYIALGTLLPFTTPYVTTSPMSPTSYMDLQASNLLNSNSILKSPESYTFTTPPEYE
TWNPKMLRLIALNEPYSGNLQGLRNADLNCHRQARRSGLMGNFRAFLSTRIQNLDSLIKP
EDRELPITNLRGDVLFNSFNAIFNNNAQGIFLSSNSPRIISFSGKNVMNDNTWPHKIVWH
GARADSIDTNCEGWHSNFQDKVGLGSSLLGNKLLAQEMYSCQQKNIVLCIEVLSHSSSGD
IANRRKREMMQSNDDTYDNEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g11445.t2 | Gene3D | G3DSA:1.20.5.320 | - | 83 | 135 | 2.5E-5 |
| 13 | g11445.t2 | Gene3D | G3DSA:2.10.10.50 | - | 325 | 365 | 1.6E-6 |
| 15 | g11445.t2 | Gene3D | G3DSA:3.10.100.10 | - | 420 | 593 | 7.5E-61 |
| 22 | g11445.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 86 | 107 | - |
| 23 | g11445.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 235 | - |
| 25 | g11445.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 205 | 224 | - |
| 24 | g11445.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 263 | 301 | - |
| 26 | g11445.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 263 | 278 | - |
| 6 | g11445.t2 | PANTHER | PTHR24023:SF965 | COLLAGEN TYPE XVIII ALPHA 1 CHAIN B | 74 | 117 | 2.2E-56 |
| 9 | g11445.t2 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 74 | 117 | 2.2E-56 |
| 7 | g11445.t2 | PANTHER | PTHR24023:SF965 | COLLAGEN TYPE XVIII ALPHA 1 CHAIN B | 162 | 301 | 2.2E-56 |
| 10 | g11445.t2 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 162 | 301 | 2.2E-56 |
| 5 | g11445.t2 | PANTHER | PTHR24023:SF965 | COLLAGEN TYPE XVIII ALPHA 1 CHAIN B | 300 | 585 | 2.2E-56 |
| 8 | g11445.t2 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 300 | 585 | 2.2E-56 |
| 4 | g11445.t2 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 162 | 202 | 2.1E-6 |
| 3 | g11445.t2 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 260 | 307 | 6.3E-7 |
| 2 | g11445.t2 | Pfam | PF06482 | Collagenase NC10 and Endostatin | 327 | 381 | 3.6E-7 |
| 1 | g11445.t2 | Pfam | PF06482 | Collagenase NC10 and Endostatin | 415 | 592 | 4.5E-58 |
| 17 | g11445.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 29 | - |
| 18 | g11445.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 19 | g11445.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 24 | - |
| 20 | g11445.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 25 | 29 | - |
| 16 | g11445.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 621 | - |
| 11 | g11445.t2 | SUPERFAMILY | SSF56436 | C-type lectin-like | 425 | 591 | 5.02E-51 |
| 12 | g11445.t2 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 29 | - |
| 21 | g11445.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K06823 (collagen type XVIII alpha)
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.
