General information for g13728.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RB1-inducible coiled-coil protein 1.
Parent gene
- The parent gene g13728 is located on chr_1: 32092918..32095357 (+ 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 | g13728 | g13728.t1 | TSS | g13728.t1 | 32088138 | 32088138 |
| chr_1 | g13728 | g13728.t1 | isoform | g13728.t1 | 32088473 | 32093655 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon1 | 32088473 | 32088540 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS1 | 32088473 | 32088540 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon2 | 32088693 | 32088904 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS2 | 32088693 | 32088904 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon3 | 32089003 | 32089303 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS3 | 32089003 | 32089303 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon4 | 32089521 | 32090445 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS4 | 32089521 | 32090445 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon5 | 32090560 | 32090752 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS5 | 32090560 | 32090752 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon6 | 32090879 | 32090969 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS6 | 32090879 | 32090969 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon7 | 32091028 | 32091135 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS7 | 32091028 | 32091135 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon8 | 32091207 | 32091378 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS8 | 32091207 | 32091378 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon9 | 32091469 | 32092855 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS9 | 32091469 | 32092855 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon10 | 32092918 | 32093267 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS10 | 32092918 | 32093267 |
| chr_1 | g13728 | g13728.t1 | exon | g13728.t1.exon11 | 32093551 | 32093655 |
| chr_1 | g13728 | g13728.t1 | cds | g13728.t1.CDS11 | 32093551 | 32093655 |
| chr_1 | g13728 | g13728.t1 | TTS | g13728.t1 | 32093999 | 32093999 |
Sequences
>g13728.t1 Gene=g13728 Length=3912
ATGTTGTACATTTTTAATATGGACCAGGGAAAAATGATAACGTTTGATGTTAGCTTAGCT
CTAGATTCCGTTCAATCATTGAAACTGACAATTGAGAGACAACATGCGATTCCAGCTTGC
AATCAAGTGTTATTAGTAAGTGGTGGAGAAACTTTAGATGCGTCTAATCGAGTATGCAGC
TATTCTGCGGGAACAGACACAAACCCTATTTTTATGTTTAGCAATAGTCTAGAACCTCGT
AATCAACCTCAACCATGGCCGAGTATAGATGATAGTAATGAAAAAGCTGATTTCAAGAAA
GAAGTCGATCAATGTTTAGAAGTTCCACAAAATCAACTTTCTGTAAATCTAGTAGCACGC
CGTGTCCAGATAGCACAGCAAATTTATGAAGCATGCAAGGAAGAGTTAAAAAATTGTGAT
AAACTTGTGCATGAACAGCACTTACAACATCAAGGATGGATGGCCGTAATGGCGAATCTA
GAGGATATAACAGATGCCTTTGAGGATCGTTGCAATGAATTTGACAAAGTATTTAAAGAA
CACATTGAACGTCGAAAAGAATATAAAGACTATCTCGAAAGTTTTGATGATGATCTTGAA
AGACTTGCACAAATTCCAATACTCCCGCCTCTAATACAAGGTGCTGAAGATCAACCATTT
CATGCATTTGATGATGTCTATAATGATACTGGTGAATCATTTGCTGGAAATGCTGCTGCA
CAAAGGCAATTACAACAGGAATCAGGTGGAAAAGTTGAAAAAGCAGCAAGCGACACAAGT
ATGGAATCAAATAATGTTCCTGTAGAGGCAGCAGACAAGAGTGTTGAAAGAAGTCATGAA
GAGGCAATGAAAGATTCTTCCAATCAAAAAACATCATTGACACTCTTGCAATGGATATCA
TCGAATGAAAATCAGAAAACACTTAAACGAATGGCCGAGAATTGTACTCGAGAACTTGAT
GTATTTGATAAAAATGTGATGGACACACTGAAGGATGAAATTGAAAAGACCGTTGAAACG
GCAAAGCGTGAAGACATGAAAGAAATCAAAGGTTTAGAAGAACGATTACAAGGTCTTGAA
GCACTCAAACGTGATGCAAAAAAGTTATTAGCAGAACAGAATGATTTAGCTCAAGCACTT
CTAATGAATCATAATAGTGTTGCAAGGTCTGGTGATGTCTCAGTTCTTCCAGATTTGTGT
GCTCCCCATAAAAATCAATTTGCACATTTATTGAGAAATCTCAAGAAACTTCGTGACATT
CGCATAAGATGTTCGAAGGCAAAAGATGAATTATGCCGGAACTTACTTCAACGTCTTAAG
TTTGTGATCCATATCGAAAATAGAATGTGTGAAATTGATTGCAAATTACTCTTTTATCAT
CGATGTTTACGTCGTTTACAAAAGCACTTGGGAATTATCGAACAAATTCATCAAGCTCCA
TGCGTGTACGTGCAAGCAGTAACTGAGGTCGTTAGACGAAGAATTTTCTCAACAGCTTTC
TTAATGTGGGCATCTGATCTCGCTTGTCATCTTCTTACAATATACAATGAAGAAGTCATG
AGGCGCACTGATTTTCGATACTCATTCGATGGACACTTTTTAAACACACTATTCCCTGGT
ATTGACGATTTTCCACCGAAATTCGCGACGGAAGCGCCTTCTATTTTTGATTCAAATTTA
CCACAATTGTCCAAGAATGATTTAAACGAATTATCGAAGCATCTTCCAGAACTCACGAAG
AAAATTCAATTACCAAATTTGAGTGCCATTATTGATTTCTTTACGTCAAGAAGTACTCAC
AGTAATCAGGAAACGACATCGACAGGAGGAGAAGATGCTGTTAATCCGTCTAATAAAAAG
TTATTAAATGTCTTTGCCCAAATGAAAGACTTTGAAAAAGGATTTGAATCAGAAACCGAT
ACTGAAGAATATGAAAAAATTGGTCAAATGTCTATCGATAAAAAGCCCACGCATCAAAGT
ATTTGTGTAGGTACTGTTGAACCTGAATTATGTGATATGGCAACGAATATGAGTATTATA
CTGAAAAATGATAGTGAAATGGTTACAGACGACAACATGCTAGCGGGATTAGAGGTGAAT
CGTATGAAAGAAATATTGATAACAATGTATAAAATTTCACGCGATTCAGTGAATTTGTTG
AAGCAGCAAATTGTAGCATTAAAAGCAGAAGCAGTAAATGAGAATCAAGTGATCAAGTCG
CAATTAGAAACAATATTGAAATCTTATGATGATCTGAAAGTAGAAACACTAAATCATGAG
CGAGAATTGATTCAACGTTTAACAGTTGACCATGAGCTTGAAATGAATGATTTATCAAAG
AAACTCTTCATTAAAGATGATGAAATTAATACGCTTAAGAATGAAAATGAGCAACTTTTG
ATAAGGCTCAAAAATTGTGAAGAAAAACGAACGGGTGATAAAAGTGAACTTGAAAATAAG
ATACAAGAAATACAAGAATTGAAACAGAAACTTCAAGAAACAGAGAAAAAATTATCACAA
CAAATTTTAGAAAAAGATGCAGCTATCAAGGCATTAAAAGATGATCATCGAAACGAAATA
GAGTCACTTAGATGTAAATTTAAATTAATCACTTCTATGGAGAGTTCACCATCAGAAACA
AGTTTAGACAAAATTGATACAATCGACATAACAACTCATGAAACAATTATTAGACAAATG
AAGGTAAATTTCGAAGAGGAAGTGCAAAAAGCAGTTAAAGAGGCCATTGAACAAGAACGA
GCAAAAGTAGCAGCAAAAATGACAGAATCAACGAGTAAATGGTCACTTACGCCGAGCTCA
CCAGGAAAATCACCAAAGGATAATCAAGAAATTTTCAAAAGAATTCTCGAAGAAAAAGAT
CGTCAACTTGATCAAATGCGTGAGCGTGAACAATTCCTAATTAAAGAATCAAATCAATTA
AAAGAAATTATTCAATCCTTAACTGATGTTGAACTTAATGAAAGTCAAGTTTCAGTTTAT
AAGGAAAAGTTAGAACATGTACAGAGTGAAAAACGAAAACTTGAAAAAGATCTTGAGAAA
GAGAAGGCAAAGCGTGCAAAATTGAATTCACTTGCACAAGGAAATGGTGGCGTGACAATT
AATTCATGTTCAAAAGATGATATCGTACTCGTTGTTTGGAACAGTATTCATGAGCAATAC
ACAATTGTTCAAGATTCATCAATATTATATTTCCTTCATGCTGAAAGTTATAATAACTTG
AGTCTTTCAACAGTTCCTCCAAATACATGTCCGCGTGTTTGCTATTGCATTGGTCGAGTA
TTAGATAAAGAATATTGTCATGCGAAGAAAGATGAAAATCGTTATAAAGTTGGGAAAGGT
ACAAAGTTTTATCGAGTCAAAGTGCGACCACGATCACCAACGAATCGTGAAATGGATAGA
AGTACTACAGAAAGAAAGAAAATTAAAAGATCAACAGATTCTCAAAGTGATTCCTCGAAA
TCGATGAGATTAGAACGGCAACCAAATAATTTAATTGATTCTTTTGCTCAAACTGAAACT
CATACAGACACAGTAATGACAAATGTTGATATTGCAACTACATCGAGTGATATGGTTGAT
TCAGGTGTAGGCTCTCAACATAAATCATCGACATGTAAAGAACGTAATAATTCATCAATA
ATAGATGAAGATGAAGACATATCGTTTGCTGATGATCGTAATCGATATAAAAGTGTTAGC
GAAGAAGATACAGAAGAAGCAGTTGGTGCAGAATCCTCAGATATTTGTGCAATAGTAGTT
GAAGATGAAGAGAAAAAAGAAGAAGAGGCACCTGTCATAATAAAGGATCAATGTGAGATT
GCATCGCTTGATGATTCCGACGAATATCGATCACTTGAAGGCAAAGACGACACGGAGGAT
ACTGAACTTTAA
>g13728.t1 Gene=g13728 Length=1303
MLYIFNMDQGKMITFDVSLALDSVQSLKLTIERQHAIPACNQVLLVSGGETLDASNRVCS
YSAGTDTNPIFMFSNSLEPRNQPQPWPSIDDSNEKADFKKEVDQCLEVPQNQLSVNLVAR
RVQIAQQIYEACKEELKNCDKLVHEQHLQHQGWMAVMANLEDITDAFEDRCNEFDKVFKE
HIERRKEYKDYLESFDDDLERLAQIPILPPLIQGAEDQPFHAFDDVYNDTGESFAGNAAA
QRQLQQESGGKVEKAASDTSMESNNVPVEAADKSVERSHEEAMKDSSNQKTSLTLLQWIS
SNENQKTLKRMAENCTRELDVFDKNVMDTLKDEIEKTVETAKREDMKEIKGLEERLQGLE
ALKRDAKKLLAEQNDLAQALLMNHNSVARSGDVSVLPDLCAPHKNQFAHLLRNLKKLRDI
RIRCSKAKDELCRNLLQRLKFVIHIENRMCEIDCKLLFYHRCLRRLQKHLGIIEQIHQAP
CVYVQAVTEVVRRRIFSTAFLMWASDLACHLLTIYNEEVMRRTDFRYSFDGHFLNTLFPG
IDDFPPKFATEAPSIFDSNLPQLSKNDLNELSKHLPELTKKIQLPNLSAIIDFFTSRSTH
SNQETTSTGGEDAVNPSNKKLLNVFAQMKDFEKGFESETDTEEYEKIGQMSIDKKPTHQS
ICVGTVEPELCDMATNMSIILKNDSEMVTDDNMLAGLEVNRMKEILITMYKISRDSVNLL
KQQIVALKAEAVNENQVIKSQLETILKSYDDLKVETLNHERELIQRLTVDHELEMNDLSK
KLFIKDDEINTLKNENEQLLIRLKNCEEKRTGDKSELENKIQEIQELKQKLQETEKKLSQ
QILEKDAAIKALKDDHRNEIESLRCKFKLITSMESSPSETSLDKIDTIDITTHETIIRQM
KVNFEEEVQKAVKEAIEQERAKVAAKMTESTSKWSLTPSSPGKSPKDNQEIFKRILEEKD
RQLDQMREREQFLIKESNQLKEIIQSLTDVELNESQVSVYKEKLEHVQSEKRKLEKDLEK
EKAKRAKLNSLAQGNGGVTINSCSKDDIVLVVWNSIHEQYTIVQDSSILYFLHAESYNNL
SLSTVPPNTCPRVCYCIGRVLDKEYCHAKKDENRYKVGKGTKFYRVKVRPRSPTNREMDR
STTERKKIKRSTDSQSDSSKSMRLERQPNNLIDSFAQTETHTDTVMTNVDIATTSSDMVD
SGVGSQHKSSTCKERNNSSIIDEDEDISFADDRNRYKSVSEEDTEEAVGAESSDICAIVV
EDEEKKEEEAPVIIKDQCEIASLDDSDEYRSLEGKDDTEDTEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g13728.t1 | CDD | cd17060 | Ubl_RB1CC1 | 1 | 74 | 2.68779E-34 |
| 15 | g13728.t1 | Coils | Coil | Coil | 342 | 379 | - |
| 18 | g13728.t1 | Coils | Coil | Coil | 789 | 851 | - |
| 16 | g13728.t1 | Coils | Coil | Coil | 901 | 921 | - |
| 17 | g13728.t1 | Coils | Coil | Coil | 949 | 983 | - |
| 19 | g13728.t1 | Coils | Coil | Coil | 997 | 1031 | - |
| 14 | g13728.t1 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 81 | 4.1E-11 |
| 6 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 238 | 267 | - |
| 12 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 238 | 289 | - |
| 11 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 286 | - |
| 5 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 927 | 948 | - |
| 4 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 928 | 946 | - |
| 13 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1127 | 1170 | - |
| 9 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1130 | 1160 | - |
| 8 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1232 | 1252 | - |
| 7 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1277 | 1297 | - |
| 10 | g13728.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1277 | 1303 | - |
| 2 | g13728.t1 | PANTHER | PTHR13222:SF1 | RB1-INDUCIBLE COILED-COIL PROTEIN 1 | 1 | 1130 | 3.2E-173 |
| 3 | g13728.t1 | PANTHER | PTHR13222 | RB1-INDUCIBLE COILED-COIL | 1 | 1130 | 3.2E-173 |
| 1 | g13728.t1 | Pfam | PF10377 | Autophagy-related protein 11 | 1007 | 1129 | 1.0E-22 |
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:0000045 | autophagosome assembly | BP |
| GO:0000422 | autophagy of mitochondrion | BP |
KEGG
Orthology
- This transcript has been annotated with K17589 (RB1-inducible coiled-coil protein 1)
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.
