General information for g3553.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein ELYS-like protein.
Parent gene
- The parent gene g3553 is located on chr_3: 26398588..26405445 (+ 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_3 | g3553 | g3553.t1 | TSS | g3553.t1 | 26398556 | 26398556 |
| chr_3 | g3553 | g3553.t1 | isoform | g3553.t1 | 26398588 | 26405445 |
| chr_3 | g3553 | g3553.t1 | exon | g3553.t1.exon1 | 26398588 | 26398681 |
| chr_3 | g3553 | g3553.t1 | cds | g3553.t1.CDS1 | 26398588 | 26398681 |
| chr_3 | g3553 | g3553.t1 | exon | g3553.t1.exon2 | 26398759 | 26398882 |
| chr_3 | g3553 | g3553.t1 | cds | g3553.t1.CDS2 | 26398759 | 26398882 |
| chr_3 | g3553 | g3553.t1 | exon | g3553.t1.exon3 | 26398956 | 26399269 |
| chr_3 | g3553 | g3553.t1 | cds | g3553.t1.CDS3 | 26398956 | 26399269 |
| chr_3 | g3553 | g3553.t1 | exon | g3553.t1.exon4 | 26399329 | 26400335 |
| chr_3 | g3553 | g3553.t1 | cds | g3553.t1.CDS4 | 26399329 | 26400335 |
| chr_3 | g3553 | g3553.t1 | exon | g3553.t1.exon5 | 26400393 | 26405328 |
| chr_3 | g3553 | g3553.t1 | cds | g3553.t1.CDS5 | 26400393 | 26405328 |
| chr_3 | g3553 | g3553.t1 | exon | g3553.t1.exon6 | 26405390 | 26405445 |
| chr_3 | g3553 | g3553.t1 | cds | g3553.t1.CDS6 | 26405390 | 26405445 |
| chr_3 | g3553 | g3553.t1 | TTS | g3553.t1 | NA | NA |
Sequences
>g3553.t1 Gene=g3553 Length=6531
ATGTCAACAACAGAGAAATTAGAATTAATAAAAAGCATTAATATTAAAACTGGCCAACAA
GAACCGTACAGTTCACAAAATGAGCAAACACCAAACCGACTTGCTGGTTTTTTGCAAAAT
GGTAAACTATCTTGGATCGCTTATGATGCTATTTTAAGAATAATATCAACAAATACTGGA
GTTGAAATTGCCTATTATAACTTTGCAAAACACAATGGTATTGAAGGATGCCGGATAAAT
TATATAGAAGAGATAAAATATTTACCAGATCTTTGCATTATTGCTGTTAGCATGGAGTTT
GTAAATAACTCAATAGCTTCACATGATGCTGGAATGATAAGTATATTTTGTATACAAGGT
TCTAAAATATTGGGATCTATGGATATGAGTGAACATATTACATCTTGTAAATATCTTGAT
TGGGAAATTTGTCGAAGAAGTGCATTACGTGAATTTCATGGAACACTTGCTATTGGTACA
AATCAAGGAAAAATCTTTCTTGTTGATTTAATGATTCCAAACGATATAAATGAAATTGTA
CTATCAAGAAGTTATGCCGGTGAAATTTTTCCTATGGTGATTGCTCCAATGAATGATGAT
ACTAATCAAGTTCAACTTATAAATCTTCATAAAAAGTTTATCAATACTCGAGACTCAATC
GGTGAACGAAGTTTTTTTGCAATACAACTAAAACAAGTTTTAGACGATTCAGGAGCTATA
ATTTCATTTCTTTGTATGCCATCTTTAATCATGATGGCAACAGGACTTGCTGATGGCCGA
ATGATTTTATATGATTTAGTTGATTTACAAGCATTTCATCTTGCTTATCCGCCTGGAAAT
TGTTCACCATTAACTCACATGTCATTTATTGAACCTGCAGATGATCCAAGAAGTGCTATC
TATATTTGGGCTTTTCACGCTTCAAAAGATGGAGCAATTGCAGTAATGCACTCAATAATG
TTTGAAAATCGAGTAAATGGATATTATGAAAACTTTCGTTCATGCAGCGTTCGTCTCACA
ATGCCAATGTTTACAAAGGATACATTTCCAGTTTGCTGTCGTTCAATTACAAAAAAATTA
TCTGAAGAAGACGAAATAATTACAATAAACTTACTTGTTTGGACATCACCTTCACGTAAT
TTGACAAATGTAATGATATTCGATTTGAATCAATGGTATAAAGAAGAAATGCCTAGTGTT
GGTGATTGGCGTAATCATTTAAAATATGCAGTTGTTTTTGAAGTTCAAAATATTGCACTG
GATACATTACTCAATGAACAATCAGTTATGCCATTTAATTCTATAAGTCGACCTGAAGAG
CATTTTTATCCAAATTCCTTAAGCTTTGATATAGTTGTTCTTGAAATCAAAAGATTTACT
CATTACCATTGGGTTGGTGCACAAAATCAAGTGTTACAGCAATTTCACATTGTCGGACCA
AATATGATACTCGAACCAAGTTACTATTTTAATGAGCTTCTTCAAGTTTCAATTTTACCA
CAATTTTATGATACTAATTTTAGCATAGCATCTTCAATTGAGTTAAAACGTGAATTTCTA
TTGTCGGTGGCATTAGAATACAACTTTACTGGATTTCTTATGAAATGTGCTTGGTCATGG
GCTGATGGAAGCTATATTGGAAAAGATGGAACAGGAGTAAGTCTTTCTACTCTTACAGAA
TGGATTTGGAATCGAGTACTTGCAATTAAAGAAATATCAAATACGTTAAGTCAACCACTT
TTTGATTTTTCGGAACAAAGAATTGATTGCGGAACTCAAAAGCAGCTCTCTATGTGTTGT
AAACAATTAAAAACCTTATCTGAATTGTTGCAAATAATCACAAATGATTATAAAAGATTT
ATTCCTGAAAATATTCAGTCTCGATTACAAAATCAAATGGAAACAGTTAAAATGGCTTCA
GATTATCAAGAAGTGCTTCAATGGCTATTGAATGTCGGCATGTTACCAGAAGGGAATCAA
AATTATAATAGTGAAACAGAGCTGAATGATGATTTTATTATTGTGCCCTACCCTTACCGT
ACAATTAGCTCTCATTATAATACACAAAGATTTAAATTTAATGATGATGAAGACGATCGT
AATAATTCTTTTCCGTGCAAGTATCTTTTTATTGATTTATATATCGAAAATGAATGCAAT
GGAAATGATTTGATACAAAATTGGAATGGAAATTATCCACCAAAAACAATACAATCTCTT
TTGCGAACTCTACTCGTCTCAAATATTCCAACTGAAAATAAGCATGTCATACTTATGTAT
GTTTTTATGGACATCACTAATGCACTCAATGAAACTCCATATGCAACAATTGTACGCAAT
TTAATTAAATTTCCAGCTGTTTTCAAAATTAAACCATCGACAATTAAACGCACTCAAGCT
TTTTGGAACTTAGATAATGGTCTATTAGATACTGCTGTTGAAGAGCTTATTTCACCTCTT
TCAAATGATAGATTTCTACCTAAATGGCAACGTGAATTACTAGTTAGAGCATTATTGAAA
CAAAATGCAACAAGTTTGGCATTGAGGGCTTTATGTGCTCCGGGATATCCTATAGCAGCA
GAACTCGAAATGGCTACTCTCTTATCAAATAATCTCATCAGTAAAGCTCTAAAAACTCAA
CGTGCAAGCGGTGATCGAAGTTTGTTGAAAAAATTTTTCCATACTATACTTCATTCTGCA
AATTATGAGCAACTTTTGGATTTGGCTTTAACTGAAGACGAAGGAAATGTATTGAGAGAA
TATCTTCAAAGTACAGATTTACCAAATAGTGTTAATTTACACTTTGTATATTTATTGCAA
CGTGCTAAATTTATAGATGCAGCTCGATTAATGGATTCGTTTAATAATTCAGATGCACAT
TTAAGTATGGAATCGCCTAAACATGTTCTTAATGCCTATTATTCTGTAATGGAACCAACA
ACAAGAAAATTAACTTCAATGGCTTATACAGAATCACAATCAAATTTATCACGCGTAAAT
GAACCACCGCTTCCATTAAGCGTTAGTCTCATTCGTTCAAGATGCAATGCAACAAATGAC
ATTTACAAGAAATGTGTTCAATCAATTACAGAAGCAACTCATGATACAAATCAAGAGGTA
AATGAAATTCCATTTATTGGTATGCCTAAATTAGGAATGTTTGCTCAAAAACCACATGAA
ATTCAAACTCAAGATATTATAGAACCCTTGGAATTCAATGAACATGGTAAACGAACTAAA
AACTCGAACAATGAAATTTTCCAAATGGATGTTCTTGAGGGACCACGAGCAAAACGTCGA
AAAATTGATGAAGTTCTTACATCTAATAAATTCAAAAGTTTTGTTGATCGACGTATTAAT
TTACTTACAAATTTTAAACAAACACGACCACAATTAAATTTCTCAATGAAAACACCTTCT
TCATCATCACGAGTAACCCCAGAAAAACAAATTCCAGTTCCATTACTATTTGGTGATGTT
CTTACTCCGATTGTTGAAAAGAAAACTCCTTTGAAAATTTTAGCTGATCGAGCAGCAACT
CCTCAATCTATTTTGAAAACTAAATCATGTCGTTCTAGTGTATCTCCTGCTCACAGTAGA
TATAGCGAATATGATGATAATAAATCAGTAAAATCAATTACATTCGCTATGCCAGACAAT
CGTGATCAAGATTCTTCATATCTCGATGAATCATTTGGAGAAGCAGTTCAAGTTAATTCA
TCAGCAGAAATATTTTACTCACCAGAAAAACAGACAAAAGATGATGATATTGTTGCAATT
TCTTCAAGTTCAACAATAACAAGTGGACCAAAGCCTCGGCCGTCAATTAAAAGTCATAGT
CGCTCCAATACACCAAATGAAGAGGTATTTAGTAAACAACCTCAATCAATAAGTATTAAT
AAACCTATAGAGGAGGAGGAGGAAGAAGTTAAACCGTTTACATCGCATGATGTTCGAGCA
CAATCAACACAAAAAGTTTTTGCCGAACATATTGAAAAACCTGCTTCACCTCAACAAATT
GCAGAAACTATTGAGTCTTCAAATGAATCAGAGAATAATGAAATATTTAAACGTGAGGGA
ATATTAAATTCAACTGATGAAGAAAGTGAAAGTTCTGTTAGTATACCTGATGATTCCATT
TATGGATATGTACGAAAATCTGTTCTACAAACAACAACACAAACTGATTCCTCAGACGAT
GAAGAAGAGGATGATGAGCGTGAACCATCATATAGACGAAATAATTTACAATCAAGTAGT
AGTGATGATGACGATGAAGATTTACAAATTGCAGAAGATGAACATTTTGAAGAAGAAGAA
CTGCCTGAACATAGTGATTATGATGATTATGACGAATCTTCTAGTGATAAAAGCCCTGAA
AAGAAAATTAATATCACAGAAAGTAATGAAATAATTGAATTGTTAGATTCAGATGATGAT
GATATATCTATGAATTCGCCAAAACATAATTTACCTCCATTTAATCAAATAGAATCACGC
CAAGAAATTGTTCAAAAAACCACATCAGAAAAAGATGAAATGGATGTCTCAGAATATCAA
AAATTATCTAATACTCAAAATCCAATTGATTTAAATGAATCACATTCTTTGACAAAAAGT
ACCAGTCATATTGATCCACAACAAGAAGTTTTTCAACAGACAATATCAACAAAAGAGGAT
GAGATAGAGGAAATGGATATTTTAGAATTAGAGAATGTTCAAAACACAACTGAACTAAAT
GAACCATCAACAGAAAATGAAATGATTGCATTGATTTATGATAATCTTGAAGAACAGCAG
AATGTGATCAAATCTAAGGAGTTAGAACAGTCAGTAATTGCAACAACTAGTCAAATTGAA
CCTCAACATGAAGAAATTGATCCACAAAAAGTCTTGATTAAAGAACCTGAGTCAGAAGAA
AATGTTATTGTTGAATTAGAAAATGCTCAAAATATAATCAAATCAAATCAAGTTTCATCA
GAAAAGGATATAAATGAAATGTCTGCGATGAATGAAGGAACTAAAAATATATTGGAGGTT
GCCATGATTGAAGAAGAGAGTAAAGTTGAAGAGTTAAATGTTGTTGTTACAAATGAAATG
ACTGAACTGTTAATAGAAAAAGAGATAACTGAAGTTTCCACAAAAAATGTATTGGAAGTA
GCTATAATTGAAGAAGAAAATAAAATTGAGAATACTGAAGGAATTGTAAGTGCTGTTTCT
ACCACTGAAACGCATGAATTGACAATAGAAAAGGAAATAATTGAAATTTCCACAATAAAT
GAGGAAACGAAAAACATATTAGAAGTAGCTATGATTGAAGAGGAGACTAAAGTTGAAGAA
CATAGTACTGCTACTAATGAGACACAAACAAATGAAAAAACTTTAGATATCGCCATGATT
GATGATGATAAAAATAATTCTGATATTGCTGAGAATCTTAAAATTGATATGGAAGTTCAA
GAAATACTTAAAACACCAACAAAGAATAAAGGTGAAGTTGAACCACACTCTTCACAAACT
GATACAGATTATTTGTCAACACCTAGACGAACAAGATCAGTAGCTCGTTTTGAATCAGAA
ACAGGAGACGCTCAAAAACCAATTCGTTTGTTAAGAGCAACATCAGTTCCTTCTAGTTCT
ACTTCTTCTTCGCCAGTTCCACATTCACGCTCTTCACGTGCTTCATCAGAACTTCGTACA
AATCCAAAAGCAATGATTAAAGAAAAAATGTTGGAAAGTATTGCAGAAAGTCCCGTAATG
CTCACTCGAAGTAAAGTTAGAATGCTTAATGAGAGTCGTGGAACTACGCCACAAACACCA
AATTCTCGTGCACCTTCAGAAGATCAAGACTCAGTAAAAAAGACTCCAAGACGTCGCCGA
TCTTCATCTAGTACACCAATCACTCCTCGAAGAATTTTAACCCGTGCAAGTAGTGTTGCT
TCATCTACACAAATTGATGGAGAAAAGACACCAGAAGAACCTACAAAATCAAATCTTCGT
AACAAAAAAAGTAAAATGAACAATTCAGATGATGAAGGCGAAGATACAAAATCTTTGAAA
AGTAATAAATCTACATCTTCATCACGTAAAAAAAATACTTCATCATCCAACACTAAAAAT
ACACCTAATACAAGTCCTATTATTGATGAATTAAATCAAAATACCCGACGTTTAACCCGA
GGTCAGTTAGCTGTTTTGGAAAAATCTCGCGAAGTAGCTCAGAGATTGTCATCAAGTTCC
CAATTAAGAAGAACTGTTTCCGATTATGGATCAAGGGGAAACATTGAAGAAAATGACTCT
GACAATGAAAGCGTTAAAAGTGAAAAATCAAAAGATTCCAAAAAATCTTCTCGACGAGGA
GACAGAAAACGAAAGCTTCCTTCTCATTTAAACGATTTTGAGACATCAAGTAATGCTTCT
TCACGGAAATCAAAAAGCCCTAAAAAACACCAAGATTTATCAGTAATTCCTGAAGAAAAT
GAAACGCCATCAGTACTAGAGAGATCCACTCGAAGTCAGAAGAAGAAATAA
>g3553.t1 Gene=g3553 Length=2176
MSTTEKLELIKSINIKTGQQEPYSSQNEQTPNRLAGFLQNGKLSWIAYDAILRIISTNTG
VEIAYYNFAKHNGIEGCRINYIEEIKYLPDLCIIAVSMEFVNNSIASHDAGMISIFCIQG
SKILGSMDMSEHITSCKYLDWEICRRSALREFHGTLAIGTNQGKIFLVDLMIPNDINEIV
LSRSYAGEIFPMVIAPMNDDTNQVQLINLHKKFINTRDSIGERSFFAIQLKQVLDDSGAI
ISFLCMPSLIMMATGLADGRMILYDLVDLQAFHLAYPPGNCSPLTHMSFIEPADDPRSAI
YIWAFHASKDGAIAVMHSIMFENRVNGYYENFRSCSVRLTMPMFTKDTFPVCCRSITKKL
SEEDEIITINLLVWTSPSRNLTNVMIFDLNQWYKEEMPSVGDWRNHLKYAVVFEVQNIAL
DTLLNEQSVMPFNSISRPEEHFYPNSLSFDIVVLEIKRFTHYHWVGAQNQVLQQFHIVGP
NMILEPSYYFNELLQVSILPQFYDTNFSIASSIELKREFLLSVALEYNFTGFLMKCAWSW
ADGSYIGKDGTGVSLSTLTEWIWNRVLAIKEISNTLSQPLFDFSEQRIDCGTQKQLSMCC
KQLKTLSELLQIITNDYKRFIPENIQSRLQNQMETVKMASDYQEVLQWLLNVGMLPEGNQ
NYNSETELNDDFIIVPYPYRTISSHYNTQRFKFNDDEDDRNNSFPCKYLFIDLYIENECN
GNDLIQNWNGNYPPKTIQSLLRTLLVSNIPTENKHVILMYVFMDITNALNETPYATIVRN
LIKFPAVFKIKPSTIKRTQAFWNLDNGLLDTAVEELISPLSNDRFLPKWQRELLVRALLK
QNATSLALRALCAPGYPIAAELEMATLLSNNLISKALKTQRASGDRSLLKKFFHTILHSA
NYEQLLDLALTEDEGNVLREYLQSTDLPNSVNLHFVYLLQRAKFIDAARLMDSFNNSDAH
LSMESPKHVLNAYYSVMEPTTRKLTSMAYTESQSNLSRVNEPPLPLSVSLIRSRCNATND
IYKKCVQSITEATHDTNQEVNEIPFIGMPKLGMFAQKPHEIQTQDIIEPLEFNEHGKRTK
NSNNEIFQMDVLEGPRAKRRKIDEVLTSNKFKSFVDRRINLLTNFKQTRPQLNFSMKTPS
SSSRVTPEKQIPVPLLFGDVLTPIVEKKTPLKILADRAATPQSILKTKSCRSSVSPAHSR
YSEYDDNKSVKSITFAMPDNRDQDSSYLDESFGEAVQVNSSAEIFYSPEKQTKDDDIVAI
SSSSTITSGPKPRPSIKSHSRSNTPNEEVFSKQPQSISINKPIEEEEEEVKPFTSHDVRA
QSTQKVFAEHIEKPASPQQIAETIESSNESENNEIFKREGILNSTDEESESSVSIPDDSI
YGYVRKSVLQTTTQTDSSDDEEEDDEREPSYRRNNLQSSSSDDDDEDLQIAEDEHFEEEE
LPEHSDYDDYDESSSDKSPEKKINITESNEIIELLDSDDDDISMNSPKHNLPPFNQIESR
QEIVQKTTSEKDEMDVSEYQKLSNTQNPIDLNESHSLTKSTSHIDPQQEVFQQTISTKED
EIEEMDILELENVQNTTELNEPSTENEMIALIYDNLEEQQNVIKSKELEQSVIATTSQIE
PQHEEIDPQKVLIKEPESEENVIVELENAQNIIKSNQVSSEKDINEMSAMNEGTKNILEV
AMIEEESKVEELNVVVTNEMTELLIEKEITEVSTKNVLEVAIIEEENKIENTEGIVSAVS
TTETHELTIEKEIIEISTINEETKNILEVAMIEEETKVEEHSTATNETQTNEKTLDIAMI
DDDKNNSDIAENLKIDMEVQEILKTPTKNKGEVEPHSSQTDTDYLSTPRRTRSVARFESE
TGDAQKPIRLLRATSVPSSSTSSSPVPHSRSSRASSELRTNPKAMIKEKMLESIAESPVM
LTRSKVRMLNESRGTTPQTPNSRAPSEDQDSVKKTPRRRRSSSSTPITPRRILTRASSVA
SSTQIDGEKTPEEPTKSNLRNKKSKMNNSDDEGEDTKSLKSNKSTSSSRKKNTSSSNTKN
TPNTSPIIDELNQNTRRLTRGQLAVLEKSREVAQRLSSSSQLRRTVSDYGSRGNIEENDS
DNESVKSEKSKDSKKSSRRGDRKRKLPSHLNDFETSSNASSRKSKSPKKHQDLSVIPEEN
ETPSVLERSTRSQKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1262 | 1319 | - |
| 12 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1262 | 1300 | - |
| 8 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1301 | 1315 | - |
| 14 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1331 | 1470 | - |
| 9 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1351 | 1365 | - |
| 13 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1421 | 1447 | - |
| 5 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1448 | 1467 | - |
| 7 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1825 | 1904 | - |
| 10 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1872 | 1899 | - |
| 11 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1929 | 2176 | - |
| 15 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1929 | 1946 | - |
| 17 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1961 | 1988 | - |
| 20 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1989 | 2019 | - |
| 18 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 2020 | 2060 | - |
| 16 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 2072 | 2093 | - |
| 19 | g3553.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 2094 | 2115 | - |
| 3 | g3553.t1 | PANTHER | PTHR21583 | ELYS PROTEIN | 28 | 1010 | 1.2E-129 |
| 2 | g3553.t1 | Pfam | PF16687 | beta-propeller of ELYS nucleoporin | 42 | 454 | 4.3E-8 |
| 1 | g3553.t1 | Pfam | PF13934 | Nuclear pore complex assembly | 709 | 924 | 3.5E-35 |
| 4 | g3553.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 16 | 296 | 4.73E-7 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K25129 (protein ELYS)
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.
