General information for g13663.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AT-rich interactive domain-containing protein 4B.
Parent gene
- The parent gene g13663 is located on chr_1: 31464051..31465299 (- 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 | g13663 | g13663.t1 | isoform | g13663.t1 | 31460092 | 31465299 |
| chr_1 | g13663 | g13663.t1 | exon | g13663.t1.exon1 | 31460092 | 31460264 |
| chr_1 | g13663 | g13663.t1 | cds | g13663.t1.CDS1 | 31460092 | 31460264 |
| chr_1 | g13663 | g13663.t1 | exon | g13663.t1.exon2 | 31460321 | 31460428 |
| chr_1 | g13663 | g13663.t1 | cds | g13663.t1.CDS2 | 31460321 | 31460428 |
| chr_1 | g13663 | g13663.t1 | exon | g13663.t1.exon3 | 31460495 | 31460617 |
| chr_1 | g13663 | g13663.t1 | cds | g13663.t1.CDS3 | 31460495 | 31460617 |
| chr_1 | g13663 | g13663.t1 | exon | g13663.t1.exon4 | 31460680 | 31463959 |
| chr_1 | g13663 | g13663.t1 | cds | g13663.t1.CDS4 | 31460680 | 31463959 |
| chr_1 | g13663 | g13663.t1 | exon | g13663.t1.exon5 | 31464022 | 31465212 |
| chr_1 | g13663 | g13663.t1 | cds | g13663.t1.CDS5 | 31464022 | 31465212 |
| chr_1 | g13663 | g13663.t1 | exon | g13663.t1.exon6 | 31465297 | 31465299 |
| chr_1 | g13663 | g13663.t1 | cds | g13663.t1.CDS6 | 31465297 | 31465299 |
| chr_1 | g13663 | g13663.t1 | TSS | g13663.t1 | 31465486 | 31465486 |
| chr_1 | g13663 | g13663.t1 | TTS | g13663.t1 | NA | NA |
Sequences
>g13663.t1 Gene=g13663 Length=4878
ATGCAAGGAATACCTCAAAAGGATAAAGACGATCCTGTTGTTTTATCAGTAGGTGCACAA
GTTAGTGCAAAATATAAAGGAGCATTTTGTGAGGCAAAAGTTCATAAGGTCGTGAAAAAT
ATCAAAGTTAAAGTCGCATTTAAAAAAGGAGGAACGGCAACTGTTACAGATGATGAAATA
ATAGGCGAAATTCGTGTTGGAAATATCGTAGAAATAAATGATGCAGATAAAAAAGAAACA
AATGAAGCAACTATCACAAAAATACAGGATTGCTCTCAATATACTGTAGTTTTTGATGAT
GGTGATATTGCAACATTAAGACGCACTGCTCTTTGTCGTCAATCGGGAAAACATTTTAAT
GCTTGTGATACTCTTGATCAATTGCCTTTGACTCATCCAGAACATCGAGGAGGAGGCAAA
CGAACTAAAACGCAAGATGAGTATGAATCAGATGATGAAGAATATGCTATAGGGAAAGTT
GTTTGTGTAGAAAACAATGATACAAAGAAGAAAAATGTCAAAGAAAGTTACTTTCCTGCA
TTAGTTGTTGCACCAAAAGCCCAAGAAAATGTAAAGATTCATATCAAAACTGAATATTTA
GTGAGATCTTTCAAAGATGGTCGTTATTATACTGTACCTAAAAAAGAGGTCACTGAATTT
ACAAATGATACTGCATCAAAATCTGATTCAACTGCTGTTGCAGCAGCTCGTGAGTTTTTG
GATAAAAATGTTCTCCCTCCACATTGGGATCGTGAAGTTTTAATTGATTCGGCTAGTTTA
AGTGATCAAGAACTTTCTGATAGTTCCGATGATGAACCAAATGAAGTTAAAGATAGATTT
TTTGCGCAATTACTTGAGTTTATGGAGAAACGAAACTCGCCTCTCAATAAAGGGCCAAGT
ATTACAAATCGAGATGTGGACTTGTATCGACTTTACTACTCAGTAGAAAAATTAGGTGGT
TATGCTAATGTCACTAAAATTAGAAATTGGAAAGCAATTGCTAAACGTCTCGGATTTACA
CCAACTGATGCAATCGTAAAATTGGTAAAGCATTCTTATAGAAAATTTCTATTAGCATTT
GAAGAAGCAGTGTCAAAAGGAATCGAGGATTTACCTCCAAGAGCCAATCGAGATAAAGCG
AGAAGTAGTTCAACACGATCTGGCTCTGTGGCATCGCCAAAAGTAGTTGAAAGTGCAAAG
AAAAAAGTTGAAAAACCAACGACAAGTAGCGTAGCGGATGATTCAGAAAATACAAGTGAA
TCTATTAAAGTTACAACTTCTCGAAAATTATCGACAGCAAGTACAAAATCGAAAGTTGAT
AAAGTAGAGGAGAAAGCAAAATCTGAAAAATTGGAAAAAGAAAAGCCGGAAAAGAATAAG
GATAATGTTAAATGTGGTGAAAAAGATAGTGATAAAATTGATAAAGAAAAATCAGTATCA
AAGGATGATGAAGTGAATACAATAGCTTCATCGCCTACACAATCAGTCACGACTGCATCA
GCAAAGAAAGAAAAAACTAAAAAGAAACCTCCAGAAAATAAAAAGAAGAAAGAAGACACT
GCTGAGAAAAAAGAAACAATAACAATAGCTGCGAAAATTCAAGTACCTTCGGGACCAAGT
ATTGCTGATGATGTAATTATTGAAATTGATGATCGTTTGAAAGTGTATTATCGTGGTTCT
TCTGACTATGAAGCAAAAGTGTTGAAAATCTCTGAACAAGAAGGAAAACCTGTGTATAAA
GTTCATTACAAAGGATGGAATGCTCGTTATGATGAATGGATTCATCGCGAAAGCATAGCA
GAAAACTTGACAAAGGACGAGGCGAAAAAGAAGCAATCTAGTAATAATAGCAATTCAAGT
AGTACTACTGTAAAAACTTCCAGCACTTCAAGTACAAATTTACAAACACCTACTACTAAG
AATCCAACAAAGCGTGCTCGCAATAGAGCTGATACAACTGCCTCATCGCGCTCGACTACA
CCATTATCAAATACATCAAGTAAAACTAAAATTGCACAAAAGCGACCAACTCGCGGCACG
CCAACAAGTAAAAGTTCAAATCGTGGTTCGACTATTGATGATAATTCAAGTGAATCTGAC
GAACCAATTAAAAAACCGTCAGAGAAGAAAGAAAAATTGAATGATGATAAAATTCAAAAG
TCATCATCTGTTGTTGACGTAACATCAAGTGACAATAAAGATGTATCTAAGACCGAACTG
AAAGTAATTAAAGAAATTAAATCGAGTGAAAAAGTTCAAGCTCCTGACACAACAAAATCA
GACGATGAAAAATCTACAAAGTCCTCAATCAAATCTGGAAAATCACCTTTCGATGTAAAA
GGCTCAAAAAATAAAAATATTCAACGTGATTCTAGTCGTTCGTCATTTCATTCAACTGAT
AGCGATTCATCACATTCTGTTCCAAGTGATGTACCGAATAGTTCAAAGAGCGCTTATACA
AGTGAAAATGAGTCAAATGAACCAGAAAAAATTCCAGCATCAACAACAAGTACAATAGTA
ACAACAACTGTAAAAACTGATGTTAAAAAATCCTCGTTTAGATTTGATGAAGAAACAAGT
GATATCAAAAATCCTCTTTCATTTTTTGAAAAAGCAGTGAGTGAAAAAACAGAAATTAAA
ACTGAAAGCGGAGCAATATTTCCTACGAGAAAATCGAATATTTTTCAAGATAAGAAAGCA
ACACAAAAAGCTGCTGCTGCAGATACTTCAAAACTTGGTCGTTTTGGACAATCTTTAGCA
AAAGAAATTGGCAAAGTAAAGAATAAAGATATAAAGAATGAAGATAAAACCGCTGAGAGT
GATATTTATGAGTTTAAAGACACTGAAGAATTTTCTGATGCAAAAGTTGTGAATACACCT
GTTAAAAAGCAAGAATCACCTAATGAGCCTACTAAAAAGCAACAATTAGCACAACAAAGA
AAACAAGCAAGGCAAAGTGTTATTGATACTTCTTCAACAAGCAGTCCGATGGAAGATATT
GAAAGTATGATTAAAACTTCAATAGTATCATTTCCAAATAAGAAGCAAAAGAAATCACCA
GTAAAAGAAGAAAAGGCACAGCATTCAATGATTATGGCTCGAACGCCAGCTTCAACATCC
CAAAATGTAATTATTCCTCAACCATGGAGTGCAATTCAATCAACAGCTCAAATATCACAA
GAACTTTTTCCTAAGACTAACATACCTCCTCCAATTTTATCGCAATCTCTGGTTAGTAAA
CCGAAATCAGATTCAACATTTGATGTTCTACGAAAATCACCAAGTTTCAATATGCATCAT
TCTGATGATTTCCTACCATCAAAACCATCAACTCAAACTACACCGAGAAATATTGCAGCT
GGTCCTGTGAAATTTAGCAGTGATTTAATTGAGCAACATGATTTATTAAAACCAATAATG
GTACCAAGTAAAGAGGATGAAAAACCGGAATTAGAAGCATTTAAGAAAATTCTAGAGCCA
TCTTTTGAAATTTTGCCAAAAACTGAAGTAAAAGCTTCAATTGCAGATAGATTATTAAAA
GCAATTAATCAGAAAGATGCTGCGAATGAACGTGAAATTTCTCAATATAGCGCTATAATC
AAAGATGAGCCATATGTTAAAATTGAAGAACTTAAAATGGATCAATACACGTTTAAAGCA
AAATCACCAGGAACTTCAAAGTCAACAACAATTACAAATACACTTGTTACTACAACCAAA
AAGCCCCTACTTTTATCGCCTGAAACTAAAATTGATGATAAAGCAAAGGGAAATGTTGAA
CTTCAGGGAATTATAGAAAAACTCGAAAGTGCCATTTCAACGCCAATCTCATTAACAGCA
GCAACTTCTTTGGATACTCCAACATCTACATCGTTTCCTTCTACAAAGAAACAAAATGAT
GACTCAGATACAGATTCAGATCGTTTGGTAATTGAAGATGAAGCAACACCAAATGAAACA
GCAGTAGATAAGAAAAAAGCTCCTATTGGTGCACTCGAGTCTATCATGCTACAAGACGAT
GTTCCATATAAACATAATAATCCTAGTTCGAAGGAGGCTGAAAAGAAATCTGATAGTGGT
GAACAGCAAAGTGAAACAATGTCTCTCTTACTTTGTGAAGAAACAATTCCTGGCTCACCA
GCTCCAAGTACATGCAAAGATCCACTAAGTGAAATCGGAAGGAGCCCTACTTCAGGCTTT
GTTCATCCTTCAATGCCACAAAGTGGCAGTGGATATACTATGAAATATACCGGTCCAACT
TTACTTCATCATCAATCTACATCACATCAAGGCAATATCAAGTCTTCGATTTCAATGGAT
ATAGATAGCGAAGTAGGTATAGAAGCGGCCACTGGTGATATTTTACGTGATAAATTAAAA
TCTGAACGTGGTAGTGCAACAAGCAGTGGTAACAACACAAATAACAATTCAGATAATTCT
CTTGATGATGATCAATCAGAAAGTGAAAAGAATGTTAAATCAGATATTTCACGAAAAAAG
AAAAGAACAATGAAAATTGAACCAGACATTCATGCAAAGAGACGTCGTCAACATACAAGA
CCTCAAACAAATGTTAGAGGAAATCTTCAAGGAAATGATTCTGACAGCAATGATAATTCA
GATGTGAATATTTTTACAAGAAATCAAGTTGAACCAAGTCAAGGAAGCTCTAATAAAATT
CAATTTAACTTTTTGGTTGAACTTGATCCAAATATGCCGAGTTGTCATCGTATATCACTT
CTTGAGAAGAAAATTCAGGATCTGAGAAAGACATACATGATGATTAAGAATGAAATGAAT
GCAAAAGAAAGACGACGTAAGAAAATGAGAAAACGTGAAAGAGAAAATAAGCAAAAGCAA
ACTGCAAAAGTGTCATAA
>g13663.t1 Gene=g13663 Length=1625
MQGIPQKDKDDPVVLSVGAQVSAKYKGAFCEAKVHKVVKNIKVKVAFKKGGTATVTDDEI
IGEIRVGNIVEINDADKKETNEATITKIQDCSQYTVVFDDGDIATLRRTALCRQSGKHFN
ACDTLDQLPLTHPEHRGGGKRTKTQDEYESDDEEYAIGKVVCVENNDTKKKNVKESYFPA
LVVAPKAQENVKIHIKTEYLVRSFKDGRYYTVPKKEVTEFTNDTASKSDSTAVAAAREFL
DKNVLPPHWDREVLIDSASLSDQELSDSSDDEPNEVKDRFFAQLLEFMEKRNSPLNKGPS
ITNRDVDLYRLYYSVEKLGGYANVTKIRNWKAIAKRLGFTPTDAIVKLVKHSYRKFLLAF
EEAVSKGIEDLPPRANRDKARSSSTRSGSVASPKVVESAKKKVEKPTTSSVADDSENTSE
SIKVTTSRKLSTASTKSKVDKVEEKAKSEKLEKEKPEKNKDNVKCGEKDSDKIDKEKSVS
KDDEVNTIASSPTQSVTTASAKKEKTKKKPPENKKKKEDTAEKKETITIAAKIQVPSGPS
IADDVIIEIDDRLKVYYRGSSDYEAKVLKISEQEGKPVYKVHYKGWNARYDEWIHRESIA
ENLTKDEAKKKQSSNNSNSSSTTVKTSSTSSTNLQTPTTKNPTKRARNRADTTASSRSTT
PLSNTSSKTKIAQKRPTRGTPTSKSSNRGSTIDDNSSESDEPIKKPSEKKEKLNDDKIQK
SSSVVDVTSSDNKDVSKTELKVIKEIKSSEKVQAPDTTKSDDEKSTKSSIKSGKSPFDVK
GSKNKNIQRDSSRSSFHSTDSDSSHSVPSDVPNSSKSAYTSENESNEPEKIPASTTSTIV
TTTVKTDVKKSSFRFDEETSDIKNPLSFFEKAVSEKTEIKTESGAIFPTRKSNIFQDKKA
TQKAAAADTSKLGRFGQSLAKEIGKVKNKDIKNEDKTAESDIYEFKDTEEFSDAKVVNTP
VKKQESPNEPTKKQQLAQQRKQARQSVIDTSSTSSPMEDIESMIKTSIVSFPNKKQKKSP
VKEEKAQHSMIMARTPASTSQNVIIPQPWSAIQSTAQISQELFPKTNIPPPILSQSLVSK
PKSDSTFDVLRKSPSFNMHHSDDFLPSKPSTQTTPRNIAAGPVKFSSDLIEQHDLLKPIM
VPSKEDEKPELEAFKKILEPSFEILPKTEVKASIADRLLKAINQKDAANEREISQYSAII
KDEPYVKIEELKMDQYTFKAKSPGTSKSTTITNTLVTTTKKPLLLSPETKIDDKAKGNVE
LQGIIEKLESAISTPISLTAATSLDTPTSTSFPSTKKQNDDSDTDSDRLVIEDEATPNET
AVDKKKAPIGALESIMLQDDVPYKHNNPSSKEAEKKSDSGEQQSETMSLLLCEETIPGSP
APSTCKDPLSEIGRSPTSGFVHPSMPQSGSGYTMKYTGPTLLHHQSTSHQGNIKSSISMD
IDSEVGIEAATGDILRDKLKSERGSATSSGNNTNNNSDNSLDDDQSESEKNVKSDISRKK
KRTMKIEPDIHAKRRRQHTRPQTNVRGNLQGNDSDSNDNSDVNIFTRNQVEPSQGSSNKI
QFNFLVELDPNMPSCHRISLLEKKIQDLRKTYMMIKNEMNAKERRRKKMRKRERENKQKQ
TAKVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g13663.t1 | CDD | cd16100 | ARID | 277 | 361 | 2.89986E-25 |
| 13 | g13663.t1 | Coils | Coil | Coil | 1578 | 1619 | - |
| 9 | g13663.t1 | Gene3D | G3DSA:2.30.30.1170 | - | 9 | 126 | 6.9E-43 |
| 11 | g13663.t1 | Gene3D | G3DSA:2.30.30.140 | - | 149 | 260 | 9.8E-34 |
| 12 | g13663.t1 | Gene3D | G3DSA:1.10.150.60 | - | 261 | 379 | 3.0E-29 |
| 10 | g13663.t1 | Gene3D | G3DSA:2.30.30.140 | - | 537 | 661 | 8.7E-20 |
| 35 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 371 | 523 | - |
| 31 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 410 | 433 | - |
| 23 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 434 | 483 | - |
| 28 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 484 | 500 | - |
| 22 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 501 | 523 | - |
| 27 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 605 | 838 | - |
| 36 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 613 | 643 | - |
| 25 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 652 | 693 | - |
| 29 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 694 | 719 | - |
| 37 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 732 | 769 | - |
| 30 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 770 | 838 | - |
| 33 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 954 | 1040 | - |
| 38 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 959 | 1014 | - |
| 21 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1284 | 1308 | - |
| 26 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1336 | 1365 | - |
| 34 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1345 | 1361 | - |
| 24 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1461 | 1539 | - |
| 32 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1464 | 1481 | - |
| 18 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1483 | 1514 | - |
| 19 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1522 | 1539 | - |
| 20 | g13663.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1600 | 1625 | - |
| 5 | g13663.t1 | PANTHER | PTHR13964 | RBP-RELATED | 10 | 890 | 2.5E-162 |
| 4 | g13663.t1 | PANTHER | PTHR13964 | RBP-RELATED | 954 | 1621 | 2.5E-162 |
| 2 | g13663.t1 | Pfam | PF08169 | RBB1NT (NUC162) domain | 154 | 247 | 1.8E-27 |
| 3 | g13663.t1 | Pfam | PF01388 | ARID/BRIGHT DNA binding domain | 277 | 361 | 3.5E-19 |
| 1 | g13663.t1 | Pfam | PF11717 | RNA binding activity-knot of a chromodomain | 552 | 600 | 4.9E-10 |
| 39 | g13663.t1 | ProSiteProfiles | PS51011 | ARID domain profile. | 274 | 365 | 26.973 |
| 17 | g13663.t1 | SMART | SM01014 | ARID_2 | 271 | 361 | 1.3E-26 |
| 16 | g13663.t1 | SMART | SM00501 | bright_3 | 275 | 366 | 1.7E-23 |
| 15 | g13663.t1 | SMART | SM00298 | chromo_7 | 562 | 614 | 1.3E-5 |
| 6 | g13663.t1 | SUPERFAMILY | SSF63748 | Tudor/PWWP/MBT | 64 | 116 | 6.22E-5 |
| 8 | g13663.t1 | SUPERFAMILY | SSF46774 | ARID-like | 272 | 373 | 3.66E-24 |
| 7 | g13663.t1 | SUPERFAMILY | SSF54160 | Chromo domain-like | 547 | 615 | 3.16E-15 |
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:0003677 | DNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K07874 (Ras-related protein Rab-1A)
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.
