General information for g15887.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Spatacsin.
Parent gene
- The parent gene g15887 is located on chr_4: 7185001..7186037 (- 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_4 | g15887 | g15887.t1 | isoform | g15887.t1 | 7180395 | 7186037 |
| chr_4 | g15887 | g15887.t1 | exon | g15887.t1.exon1 | 7180395 | 7182142 |
| chr_4 | g15887 | g15887.t1 | cds | g15887.t1.CDS1 | 7180395 | 7182142 |
| chr_4 | g15887 | g15887.t1 | exon | g15887.t1.exon2 | 7182350 | 7183475 |
| chr_4 | g15887 | g15887.t1 | cds | g15887.t1.CDS2 | 7182350 | 7183475 |
| chr_4 | g15887 | g15887.t1 | exon | g15887.t1.exon3 | 7183536 | 7185422 |
| chr_4 | g15887 | g15887.t1 | cds | g15887.t1.CDS3 | 7183536 | 7185422 |
| chr_4 | g15887 | g15887.t1 | exon | g15887.t1.exon4 | 7185498 | 7186037 |
| chr_4 | g15887 | g15887.t1 | cds | g15887.t1.CDS4 | 7185498 | 7186037 |
| chr_4 | g15887 | g15887.t1 | TSS | g15887.t1 | 7186173 | 7186173 |
| chr_4 | g15887 | g15887.t1 | TTS | g15887.t1 | NA | NA |
Sequences
>g15887.t1 Gene=g15887 Length=5301
ATGGACATAAAATCAAATGAATTTAAAGCAATCGAAACATTGTGGAAAACTCTTGATGAC
AGTTCAATAATTCGTGATGTTCTTTTTAAAGGAAAATACATTTCAAATGCCATCAAATTT
ATCAGTGAACGAAATCAAATCACAATCGATGAAGCCAAAGAATCTTTTTTACAAATATGT
GACAATATTGTCAATATTCTCATCCAAAATAAACAACTTTATCGTGCCAGTCATGTTCTC
AAAAATGCACAAATCAATGAACTTCATTATTTATTTGATCTTCATCAAAAGACTGATGAT
GAAAAAAAGAAATCAATCATTATTGAATATTTACAAAAGATAAAAGAAAATTTTGATGAT
GATTTAAATGAATTGGAAGCTTTTCACATTTGTTACAAAATGCTACAGGAAAACTTTTAC
ACTCATATGAAATATTTAGAAACTACAAATAAAAATCATAATAATTATGTTGTGACAGTA
AATAACATTGAAAAATTATCATTTCCAACGTATATGAAGCAATCATTGGCATGGAGAAAA
GAAATAGCAGTGGACATTTTCTTCAAATCCCAAACAGACACTGAAATTCTCAAAATAATT
CCAATTCTCAACAAGTCAATATTTTTCGGATATCTTCTTCAAAATCGACTCACAGGACTT
CTTCGTACATGGCTAAACGAACAATATTGCTCCATGGCAGGACAAACCATTCGATCAACT
TTAAATTCACCACAAAATTTTGATGAAGCTTTAAATTTTCTTTTTCGAAAGTGGACATTC
GAACCATTTATGATGAATCAAATTACAAGAAAAGAGAAAGAAGTGATAAAAAATGAATTT
GCAAAACTTGGACTTTTTGAAAATCGTGAAGTGAAACAAATTGATCGAAAATTAAACCGA
TTTTTTACAACTCATACTTTTCATGAAAATTACACGACATTAAAAAGTGATGAAATTACA
AAATTTATCGTTGAAAATGAACTTTTAGAAATGTTGCCAAATAAATTTATCGATTATGAC
TGGATTAAAAATTATTTAAAAGAAAGCGATGAAAAGCAAGCAATGAGAAATGAATTGAAA
CTTTTGGGATCAACAAAAGATTTATTGACAAAAGAAACAAATTTGAATGATTTTGTGAGA
ATTTTAAATGCCACTAATGAATATCTTTTGATTTATAACAAAAACTTCAAAACTGACACA
AAAGAAATGAAATTTTTCAACGATATTGTCAAAATTAAACCTCAAGAATTTCATAAAATC
TCAGATTTGAATTTCTTTACAAAAAATTTAAATACAAAGTTAGAAAATGAGGAGAATTTG
GAAACAATTGAAGAAATTCTTGAAGAATTTCAATCGATAAATATCAAATATATTTTTGAT
GAATTTCAATCAGAACCGCATTTTGATGATCCTCAAATTTCTTTAGCTTATGGTGATAAA
GTAAAATTAAATTTCATCAATTATGTCGAAAGAGGACAAGGAACTTTTGCAACTTTTAAT
TTCATCAATGAAATGACAAAAAATTTCAACACTTTAAATCGTCAAATGATTTTAGGAGCA
TGTGAAGAAGTTGCAAAATTAGCTATGGAAAATCCAGAAAATGAAAAACTTGTAACTCAT
GTGATGGCATTTTTAGAAAGTTTCACAGTTGATACAAGAAATTTGAGATGTTTTTTAAGA
TTGCTTAAATTAAGAAATGAAAATGAAACAAAAAATTTTGAAGATTTTTTGGATGCAAAT
ATAAAAGTTGGTGAAAATTTAAATGAATCGATAAAAAACATTGAATCACTGGAAGTTTAT
TGGAAAACTAAGAAAATTTCTAATCCACCTCGTTCGTATCTTAATCAATTCATAAAAGTC
AACGATTGGTTTCATTTTTTGCTTTTCTGTCAATATTTAAAATTTCCTTTAAATGAATTC
ATTGAAATTTGCCAAAAGAATTTTCCAAACAAAAATCTTGGTGAAAATTTAATTCGTGCT
ATAAAATATGAAGCACCAGAAGAAGCCAAAAGAAGTCTTTATTTTACAAAAGTCAACAAA
ATTCCAGAAACCAGTGAAATTTTTGAAAATGGAAAATTTCTCGATTCAAATTTTGATTTA
TTTGCAATTTTACTAAAATGCAATGAAAAAATTTCACGACATGAGATGAAATTTGAAGAT
TTTGTGAAAATGTTTGAAAAAATCGATGGAGAGTTTACTAAAAATGATCTTCTTTATCAA
GCAATTAAATTTGATTGGCCTGTAATTGCAGTTTTAGCAGCAACAACAAAATTGTATCGA
TTTAAATATTGTTGGCTTACTTGGCTTATTTTGAGTACAAATTATGAAGTCAAAAAAAGA
TATGAAGATATTGAAAAAATGGCTAAAGATGTTGTTTTGAATACTATCAAAATTGGATTT
ATAAGAACATTAGAAGAAAGTGCTCAGATTTTTTATCCATCAACACCATTCAACACTTTA
ACAACATTCCTTCATGAAACTTTATCATCAAATTTCACTGAAATGGATTCAAAACTAAAA
GTCTGCATAATTCAACTAAATAAAAATAATTACAACATGACAGCTGTCAAAGGACGTCAA
AATGTGATTCCTTTTACAATTCGATGTTTAATTTCACATCTTCAACATAATATAAAATTT
ATAACAAATCAAGAGCAATATTTGGAATGCCTTCATCAATCTGAAATTTCACAATTTGAT
GATGGTCAAACTGATTTTCAACTTATGCAGCGTGTTTGCAAACTTTTGCAATTTACAAAT
GTTCAAGTGAATTATGAAAATTTTGATGAAAATGAAATAAGCAATATTTGTGATCAATTA
ATTGCCAATAATTATTTTGAAGCTGCAATTGAAGTTGCAAGTATGATGGGAAAATCAAAA
AGTGATTTCATTTTCAAATGGTGGCTGCATATGCATAAAAGTGAAGAACAACGTCAAACA
AGTTTTGATTTTGAAAAATATTTAAAATATGTCGAAACTTATGGACTTGAAATGCAAACT
TTTGTAAGATTTTTGAGATTTATCACAGCAGAAATGACAGAATGTTTGGATAAATTTAAC
ATCATGATTTTTATCTTCCGACAATTTCCAACTGATGAACTTGAATTTCAAATTCATAAT
CTTTATATTAAATTAAGAGCGAGCGGAATTGAAAATATTCAACCATTAACTTCCGACTAT
TTTGAAAATGTCATCAAAAAAGAAAAATTTTTAATCCATGAATGTCTTTATGAGCTCAAG
TCAATTGCTAAAATTGATGAACTTTTAATAAGTCAAAGAAATCTCGAAAATGAAAATGAA
ATTAAAATTTTGGATGAATTAATTTGCAAACTTCTTGATATGAATGACATAATTGAAGCT
TTAAGAGTTCATGAAATGTTCGGATATGCTCCAGAAGATTTAAAACTTTTGGCTTACATG
TTGAGTGTTTGTGAAGGTATTTCTTCAATTTATGACATTACTAAGCAGGAGAGGCAAATT
ATTAGTAATTATGCACAATTGTCTAATAGATTTAATCGATTCACATTAAGACCATTGAGG
ACTAGTAGTTGCAATGAATCAATGGACAATTCAATGATATCAATGGACATGTCAGAAAGT
GCAGTTTTTGATGAACCAACACCTTACAAAGAAAATAAAGAAACATTCCAAGCCATTCAA
GGTCTTGTTTGTAAAATCAAACATGGAAGAAGTCATGGACATCGAGCAGTTCTCATTTAT
AGAGCTTCGTTAATTCTCAATCGATCATTTAGTGAATTGATAAAAATCAAAGATCCAATT
GAATTTTTGGAACTTGCAGCAGCATGTGAAAGTGATCAGAAACTTTTAGTTATGAATGAC
ATAGTTGAAGCAATGAATTTATCAAATCACAGCATTACACAGTTTATAGCTAAAGAAATT
ACGATTTCAATTATTAAGACAAGATTTTTACAATTCAACAAAGACACAGATTTGACAACT
TCAACTTCATCTTCTTCATGGAATCAAGTTTTTGATGATATTTGGGGATTTAGTTTATCA
AAAGATCTTCATTTAATTTTAGAACTTTGCAAAGGAAAAACAACACTTTTGGGAACATAT
TTGCTTAAATTTTATGAACTTCTTTCACAACCATCACTTGACATTCCTTTTGTTCATCTT
GAATATCAAAATCTTTGTGATCAACTCAATCGTTCACTTAGTCCACAAGTTTTATCACTT
TCAAAACAAAACAAAATCAAACTTGAACTTTTAATTGTCGCACATGATTGTTTTTGTCAA
GAATGTTCAACTGAAGGAATTGGAGAAATTTTAAGATTAGCTAAAAAATTTGTCAACGAT
TTACCAAAAGAAAGTTCAAATTTGATTGTAAAACTTTTATGTGGAATTGGAAGATATCGT
GAAATGTTTTATTGTTTTGATATTTTGATTAAAAATGAAGCATTTGAGGCACTTTTGGGA
CAATTTAGTGAACGTCAATCAAGTGGATTGAAGACAGCATTGTTGAGTTATTTGAATGAA
TTTCATCCTAATAATATTGAATATTATAAAATGGCTGCATCAAGATTTCAAATGTACACA
GAATTATCAAAAATTTGGCGAACAAGTGCACTTGGAAAAATTGATAAAATTTTAGCTGAA
AATCAAATAAAAGTTCAAAAATCAGCAAGAATTTTCACAACTCAAATACAAAATCTTGAA
GTTCCATATTTGAAATGCAGTAGAAATTTGATAGGAAATTTTCATGATGCTTTAAGTGAT
ATGGTTCATGCAACTGAAGTTCTTTCAACTGAAAACAAAATTGAACTTGCCATAAAATAC
ACAAACTTCTGTGAATTGATCGCAGTTCAAATTCATTTAGTAAAAATTGCTGTTGAAAAT
GAAACAAAACTTTGCCCAAGTATTTTACAAATTGAAAAAAATCAAAAACTCTCGCAATTT
TTTGCTAATTATGAACTTTCAGTTCCACAAATGATGATTTTGAATAAAAATCTTGAAAAT
ATTAAGATCGGTTATGCAAAAGTAATTTTTTGTCGATCTTTAATTGTTGGTGATGAAATG
TTTTTACAAGAATTTATTGGAAGACTTGAATTAAGTGATGCTGTCATTGAAAATATCATA
AAACTTGCTCAATATGAAACAATCACGAAAAAACAAGAAAAAATTTTGCATGATTTAGTT
TTAATGATTCGTGATGTTGGAATTAAATTTAGACTTGCTTCTTTATTGGGATTGAAAGGA
ATACTTCAAAAATTATTGAATGATGAACAAAGTTATTATTATTTATTGGATACTAAATAT
GGTGCTATTGATATTCTATGA
>g15887.t1 Gene=g15887 Length=1766
MDIKSNEFKAIETLWKTLDDSSIIRDVLFKGKYISNAIKFISERNQITIDEAKESFLQIC
DNIVNILIQNKQLYRASHVLKNAQINELHYLFDLHQKTDDEKKKSIIIEYLQKIKENFDD
DLNELEAFHICYKMLQENFYTHMKYLETTNKNHNNYVVTVNNIEKLSFPTYMKQSLAWRK
EIAVDIFFKSQTDTEILKIIPILNKSIFFGYLLQNRLTGLLRTWLNEQYCSMAGQTIRST
LNSPQNFDEALNFLFRKWTFEPFMMNQITRKEKEVIKNEFAKLGLFENREVKQIDRKLNR
FFTTHTFHENYTTLKSDEITKFIVENELLEMLPNKFIDYDWIKNYLKESDEKQAMRNELK
LLGSTKDLLTKETNLNDFVRILNATNEYLLIYNKNFKTDTKEMKFFNDIVKIKPQEFHKI
SDLNFFTKNLNTKLENEENLETIEEILEEFQSINIKYIFDEFQSEPHFDDPQISLAYGDK
VKLNFINYVERGQGTFATFNFINEMTKNFNTLNRQMILGACEEVAKLAMENPENEKLVTH
VMAFLESFTVDTRNLRCFLRLLKLRNENETKNFEDFLDANIKVGENLNESIKNIESLEVY
WKTKKISNPPRSYLNQFIKVNDWFHFLLFCQYLKFPLNEFIEICQKNFPNKNLGENLIRA
IKYEAPEEAKRSLYFTKVNKIPETSEIFENGKFLDSNFDLFAILLKCNEKISRHEMKFED
FVKMFEKIDGEFTKNDLLYQAIKFDWPVIAVLAATTKLYRFKYCWLTWLILSTNYEVKKR
YEDIEKMAKDVVLNTIKIGFIRTLEESAQIFYPSTPFNTLTTFLHETLSSNFTEMDSKLK
VCIIQLNKNNYNMTAVKGRQNVIPFTIRCLISHLQHNIKFITNQEQYLECLHQSEISQFD
DGQTDFQLMQRVCKLLQFTNVQVNYENFDENEISNICDQLIANNYFEAAIEVASMMGKSK
SDFIFKWWLHMHKSEEQRQTSFDFEKYLKYVETYGLEMQTFVRFLRFITAEMTECLDKFN
IMIFIFRQFPTDELEFQIHNLYIKLRASGIENIQPLTSDYFENVIKKEKFLIHECLYELK
SIAKIDELLISQRNLENENEIKILDELICKLLDMNDIIEALRVHEMFGYAPEDLKLLAYM
LSVCEGISSIYDITKQERQIISNYAQLSNRFNRFTLRPLRTSSCNESMDNSMISMDMSES
AVFDEPTPYKENKETFQAIQGLVCKIKHGRSHGHRAVLIYRASLILNRSFSELIKIKDPI
EFLELAAACESDQKLLVMNDIVEAMNLSNHSITQFIAKEITISIIKTRFLQFNKDTDLTT
STSSSSWNQVFDDIWGFSLSKDLHLILELCKGKTTLLGTYLLKFYELLSQPSLDIPFVHL
EYQNLCDQLNRSLSPQVLSLSKQNKIKLELLIVAHDCFCQECSTEGIGEILRLAKKFVND
LPKESSNLIVKLLCGIGRYREMFYCFDILIKNEAFEALLGQFSERQSSGLKTALLSYLNE
FHPNNIEYYKMAASRFQMYTELSKIWRTSALGKIDKILAENQIKVQKSARIFTTQIQNLE
VPYLKCSRNLIGNFHDALSDMVHATEVLSTENKIELAIKYTNFCELIAVQIHLVKIAVEN
ETKLCPSILQIEKNQKLSQFFANYELSVPQMMILNKNLENIKIGYAKVIFCRSLIVGDEM
FLQEFIGRLELSDAVIENIIKLAQYETITKKQEKILHDLVLMIRDVGIKFRLASLLGLKG
ILQKLLNDEQSYYYLLDTKYGAIDIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g15887.t1 | PANTHER | PTHR13650 | UNCHARACTERIZED | 465 | 970 | 0 |
| 4 | g15887.t1 | PANTHER | PTHR13650:SF0 | SPATACSIN | 465 | 970 | 0 |
| 3 | g15887.t1 | PANTHER | PTHR13650 | UNCHARACTERIZED | 1123 | 1756 | 0 |
| 5 | g15887.t1 | PANTHER | PTHR13650:SF0 | SPATACSIN | 1123 | 1756 | 0 |
| 1 | g15887.t1 | Pfam | PF14649 | Spatacsin C-terminus | 1386 | 1701 | 0 |
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 K19026 (spatacsin)
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.
