General information for g6445.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein transport protein Sec24C.
Parent gene
- The parent gene g6445 is located on chr_2: 17090663..17091234 (+ 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_2 | g6445 | g6445.t1 | TSS | g6445.t1 | 17086405 | 17086405 |
| chr_2 | g6445 | g6445.t1 | isoform | g6445.t1 | 17086889 | 17090803 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon1 | 17086889 | 17086939 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS1 | 17086889 | 17086939 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon2 | 17086998 | 17088462 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS2 | 17086998 | 17088462 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon3 | 17088536 | 17088651 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS3 | 17088536 | 17088651 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon4 | 17088706 | 17089243 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS4 | 17088706 | 17089243 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon5 | 17089303 | 17089632 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS5 | 17089303 | 17089632 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon6 | 17089693 | 17089904 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS6 | 17089693 | 17089904 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon7 | 17089966 | 17090353 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS7 | 17089966 | 17090353 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon8 | 17090416 | 17090609 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS8 | 17090416 | 17090609 |
| chr_2 | g6445 | g6445.t1 | exon | g6445.t1.exon9 | 17090663 | 17090803 |
| chr_2 | g6445 | g6445.t1 | cds | g6445.t1.CDS9 | 17090663 | 17090803 |
| chr_2 | g6445 | g6445.t1 | TTS | g6445.t1 | 17091232 | 17091232 |
Sequences
>g6445.t1 Gene=g6445 Length=3435
ATGAATCCTTATGGACAACAGCAACCACCACAACAAGGATGGCCTGGAAATATCAATCAG
CAAATGGCAAATATGAATTTAGGACCACCTAAGCCACAACAACAACAATTAGGAAATCCC
CAGATGATGAGTCAAATTCCACCTCAATCATTTGCAATGAATAACAACAATCAACTTCCA
CCACCATCATCAACACCACAAATGATGAATCCTCCTCCTCCTTCTGCTGCTGCGACAATA
CCGAATAATAATAACAATATGAATGTGAACAACAACAATAATCAATTTCCGCCACCAATG
GGTCAAACAAATGGCATGCAAAATGGTTCACAATTTCCACCAGTGATGGCAAATAAAACA
ACTGTACCAAGTCAATTTCCACCAACTTCAAATGCTACATTAGCACAAATGAACACTGCA
CCTTTAATTCCTCCTTCTACTCATCAATTGCCACCACCGCCTACAATGTCACCACAGCCT
CCTGTTCAAAATTCAGGAGCTTTTTCACAGAGACCACCAGTAATTCCTGGCGAAGCTAAT
TCTAATTTACAAAACGGTGTTCAAACTAATGGAATGATGCCACCTGCACCTTCAACTACA
CAGCAAGCATCAACAATTGCTGCACCTTTGCCGCAAGCTCAGCAAACAAGACAGCCTCCA
AATATGGCATCACCACCACAATTTATGAATCAACAACAGCCAAGTTCAATGCCTCCGCAA
TTAGGCATGCCTCCAATGCCTCAAACACAACAGGCTGTTCCATTTAGTCAACCTCAAGTT
GGAATGCCTCCAATGCCCATAAATCAACCACAATTTTCATCTAATATGCCCCCGATGCCT
CCAATGCCTGGAATGAATCAACAACAACAACAATTTCAAAGTCCTATGCAAGGAGGACAG
CAATTTGGCGCACAAGCTCAAACACAGCCAAATATGCCACCAATGCCAGGTCAACCTTTT
CCTGGAATGCCCAATTCTCAACAATTTGTTCAATCACCAACAGCTAATCGAAATTTTAAT
CAACCGCCTGGAATGTATCCAAGTGCTCAACCTAGTGCACCACATCCTGGTTATCCAACA
GGTCCAATGCAGCCAGCTGCTCCACAAAAACGTTTAGATCCTGATCAAATGCCCAATCCC
ATTCAAGTTATGGCAGAAAATCAACGTGCTTGTGGCGGTGTTTTTTCGACTCTTCAAGTA
GGTCAAGTTCCACCGCTAGTTACAACAAAATTCATTACACAAGATCAAGGCAATTCAAGT
CCAAGATATATTCGTTCGACAATGTATAGCATTCCAGCAACAACTGACATGATGAAACAA
AGCGCAATTCCATTCTCGCTCATTATTAGTCCATTTGCAAGAATTGCTGATCAAGAAATG
CAACCTCCTATTGTTGATTTTGGTGAAATTGGTCCAATCAGATGTATTCGATGCAAAGCT
TATATGAGTCCACATATGCAATTTATTGACGCAGGAAGAAGATTTCAATGTTTATTGTGT
AAAGCAACAACGGAAGTTCCAGCTGAATACTTTCAACATTTGGACCATACAGGTCAGCGT
GTAGATAAATATGAAAGACCCGAATTAGTTTTGGGAACATATGAATTTGTTGCGACAAAA
GATTACTGCAGAAATAATACTCCACCTAAACCACCAGCAATGATCTTTGTTATTGATGTC
TCATATAATAATGTGAAATCTGGACTTGTTCATTTACTTTGTTCGCAAATGAAACGAATC
ATTAAGAATTTGCCAATTGATCAGGGTCATACAAGTACGAAAATGCGTGTTGGTTTCATT
ACATACGACAAATCTGTTCATTTCTACAATATTAAGAGCTCTCTAGCTCAACCTCAGCAA
TTAGTTGTTGGTGATATTCATGAAATGTTTATGCCACTACTCGATGGATTTTTAGCTGAT
CCAGTAGAATCAGAAGCTGTCATTGATCAATTAATGGATCAAATTCCTAAAATGTATGGC
GAGACACGAGAAACTGAAACAATTTTAATGCCAGCTATTCAAGCCGGTCTTGAGGCTTTA
AAAGCTTCAGAATGTGCGGGAAAATTGTTAGTTTTTCACTCAACTTTACCTATTGCTGAT
GCTCCCGGTCAACTTAAAAATCGTGATGATAGAAAATTATTAGGAACTGAAAAAGAAAGA
ACTGTATTGACACCACAAAATACCACATATAATAATTTGGGACAAGATTGTGCAGGCGCA
GGATGCACTGTTGATTTATTTTTATTTAACAACGCATATATTGATTTAGCAACAATTGGT
CAAGTTTCTCGTTTAACTGGCGGTGAAGTATATAAATACACTTACTTCCAAGCAGACATC
GATGGTGAACGATTAATATCAGACATTTCAAAAAATATTTCTCGTCCTGTTGCATTTGAT
GCAGTTATGAGAGTTAGAACATCGACAGGTACAAGACCAACAGATTTCTTTGGTCATTTC
TTTATGTCAAATACTACTGATATGGAAATTGCTGGAATTGACTGCGATAAATCAGTTGCA
GTTGAGATAAAACATGACGATAAATTACCTCCAGAGGAAAATGTCTATGTTCAAGTTGCT
CTTCTTTATACATCATGTAGTGGACAACGAAGATTGCGTATTATCAATCTTGCACTTAAA
ACATGCACACAATTGGCAGATTTGTTTAGAAGTTGTGATTTGGATACTTTAATTTTATTC
TTTGCTAAACAAGGAATATTTAGACTACTTGAGCACACACCGAAAGTATTTCGAGATAAT
TTAGTGAATCGTGCTGCACAAATTCTTGCATGTTATAAGAAAAATTGTGCATCACCAACA
TCAGCTGGTCAACTAATATTACCAGAATGTTTGAAATTATTGCCACTATACATCTCTTGT
TTGCTAAAAAATGACGCATTCTCAGGTGGCTCAGATATTACTCTCGATGATCGCTCATAT
GCGATGTATTTTGTGTGTACTATGGATTTGCCAACTTCAGTCTCATTCTTTTATCCAAGA
CTGATTCCTATCAATAATGTCAATGTCGATGAGGAAGGCATTCCACCTGCAATTCGTTGC
ACAATTGATAAAATGGCAGATGATGGTGCTTACATATTGGATAATGGTGTGTATATGTTC
TTGTGGCTTGGTGTTGGTTTATCAAGTGAATTTACACAATCAGTTTTCGGTGCACAATGC
ACTCAACAAATTGATACAGAGAGAACTGGATTACCAGTTTTTGATAATCCGTTGTCAAAG
AGAATACGTGGCATTGTGGAAACAATTCAAAAAGAAAGAACGCGTTGCATGAGGATTGCT
CTTGTTCGTCAACGAGATAAATTAGAATCGGTGCTTAGACATTTCTTGATTGAAGATAGA
GGCACAAATGGATCAGATAGCTATGTCGATTTTCTATGTTTTATGCATAAAGAGATTCGT
TCTCTTTTAAGCTAG
>g6445.t1 Gene=g6445 Length=1144
MNPYGQQQPPQQGWPGNINQQMANMNLGPPKPQQQQLGNPQMMSQIPPQSFAMNNNNQLP
PPSSTPQMMNPPPPSAAATIPNNNNNMNVNNNNNQFPPPMGQTNGMQNGSQFPPVMANKT
TVPSQFPPTSNATLAQMNTAPLIPPSTHQLPPPPTMSPQPPVQNSGAFSQRPPVIPGEAN
SNLQNGVQTNGMMPPAPSTTQQASTIAAPLPQAQQTRQPPNMASPPQFMNQQQPSSMPPQ
LGMPPMPQTQQAVPFSQPQVGMPPMPINQPQFSSNMPPMPPMPGMNQQQQQFQSPMQGGQ
QFGAQAQTQPNMPPMPGQPFPGMPNSQQFVQSPTANRNFNQPPGMYPSAQPSAPHPGYPT
GPMQPAAPQKRLDPDQMPNPIQVMAENQRACGGVFSTLQVGQVPPLVTTKFITQDQGNSS
PRYIRSTMYSIPATTDMMKQSAIPFSLIISPFARIADQEMQPPIVDFGEIGPIRCIRCKA
YMSPHMQFIDAGRRFQCLLCKATTEVPAEYFQHLDHTGQRVDKYERPELVLGTYEFVATK
DYCRNNTPPKPPAMIFVIDVSYNNVKSGLVHLLCSQMKRIIKNLPIDQGHTSTKMRVGFI
TYDKSVHFYNIKSSLAQPQQLVVGDIHEMFMPLLDGFLADPVESEAVIDQLMDQIPKMYG
ETRETETILMPAIQAGLEALKASECAGKLLVFHSTLPIADAPGQLKNRDDRKLLGTEKER
TVLTPQNTTYNNLGQDCAGAGCTVDLFLFNNAYIDLATIGQVSRLTGGEVYKYTYFQADI
DGERLISDISKNISRPVAFDAVMRVRTSTGTRPTDFFGHFFMSNTTDMEIAGIDCDKSVA
VEIKHDDKLPPEENVYVQVALLYTSCSGQRRLRIINLALKTCTQLADLFRSCDLDTLILF
FAKQGIFRLLEHTPKVFRDNLVNRAAQILACYKKNCASPTSAGQLILPECLKLLPLYISC
LLKNDAFSGGSDITLDDRSYAMYFVCTMDLPTSVSFFYPRLIPINNVNVDEEGIPPAIRC
TIDKMADDGAYILDNGVYMFLWLGVGLSSEFTQSVFGAQCTQQIDTERTGLPVFDNPLSK
RIRGIVETIQKERTRCMRIALVRQRDKLESVLRHFLIEDRGTNGSDSYVDFLCFMHKEIR
SLLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g6445.t1 | CDD | cd01479 | Sec24-like | 549 | 797 | 1.408E-108 |
| 20 | g6445.t1 | Gene3D | G3DSA:2.30.30.380 | - | 414 | 531 | 1.2E-295 |
| 19 | g6445.t1 | Gene3D | G3DSA:2.60.40.1670 | - | 419 | 881 | 1.2E-295 |
| 16 | g6445.t1 | Gene3D | G3DSA:3.40.50.410 | - | 551 | 795 | 1.2E-295 |
| 18 | g6445.t1 | Gene3D | G3DSA:1.20.120.730 | - | 882 | 1138 | 1.2E-295 |
| 17 | g6445.t1 | Gene3D | G3DSA:3.40.20.10 | Severin | 999 | 1119 | 1.2E-295 |
| 14 | g6445.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 46 | - |
| 13 | g6445.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 211 | 238 | - |
| 15 | g6445.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 211 | 237 | - |
| 6 | g6445.t1 | PANTHER | PTHR13803 | SEC24-RELATED PROTEIN | 58 | 1140 | 0.0 |
| 7 | g6445.t1 | PANTHER | PTHR13803:SF5 | PROTEIN TRANSPORT PROTEIN SEC24C | 58 | 1140 | 0.0 |
| 1 | g6445.t1 | Pfam | PF04810 | Sec23/Sec24 zinc finger | 472 | 510 | 1.5E-12 |
| 2 | g6445.t1 | Pfam | PF04811 | Sec23/Sec24 trunk domain | 549 | 792 | 4.2E-80 |
| 4 | g6445.t1 | Pfam | PF08033 | Sec23/Sec24 beta-sandwich domain | 798 | 881 | 3.4E-19 |
| 3 | g6445.t1 | Pfam | PF04815 | Sec23/Sec24 helical domain | 893 | 993 | 2.7E-24 |
| 5 | g6445.t1 | Pfam | PF00626 | Gelsolin repeat | 1015 | 1084 | 3.1E-11 |
| 8 | g6445.t1 | SUPERFAMILY | SSF81995 | beta-sandwich domain of Sec23/24 | 251 | 892 | 1.57E-69 |
| 10 | g6445.t1 | SUPERFAMILY | SSF82919 | Zn-finger domain of Sec23/24 | 461 | 545 | 6.02E-25 |
| 12 | g6445.t1 | SUPERFAMILY | SSF53300 | vWA-like | 549 | 795 | 8.15E-63 |
| 11 | g6445.t1 | SUPERFAMILY | SSF81811 | Helical domain of Sec23/24 | 893 | 998 | 4.45E-31 |
| 9 | g6445.t1 | SUPERFAMILY | SSF82754 | C-terminal, gelsolin-like domain of Sec23/24 | 999 | 1140 | 1.1E-29 |
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:0006886 | intracellular protein transport | BP |
| GO:0030127 | COPII vesicle coat | CC |
| GO:0008270 | zinc ion binding | MF |
| GO:0006888 | endoplasmic reticulum to Golgi vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K14007 (protein transport protein SEC24)
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.
