Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative E3 ubiquitin-protein ligase MYLIP-B.

Parent gene

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 g10031 g10031.t1 TSS g10031.t1 6857255 6857255
chr_1 g10031 g10031.t1 isoform g10031.t1 6857431 6861536
chr_1 g10031 g10031.t1 exon g10031.t1.exon1 6857431 6857520
chr_1 g10031 g10031.t1 cds g10031.t1.CDS1 6857431 6857520
chr_1 g10031 g10031.t1 exon g10031.t1.exon2 6859848 6860068
chr_1 g10031 g10031.t1 cds g10031.t1.CDS2 6859848 6860068
chr_1 g10031 g10031.t1 exon g10031.t1.exon3 6860151 6861054
chr_1 g10031 g10031.t1 cds g10031.t1.CDS3 6860151 6861054
chr_1 g10031 g10031.t1 exon g10031.t1.exon4 6861119 6861411
chr_1 g10031 g10031.t1 cds g10031.t1.CDS4 6861119 6861411
chr_1 g10031 g10031.t1 exon g10031.t1.exon5 6861473 6861536
chr_1 g10031 g10031.t1 cds g10031.t1.CDS5 6861473 6861536
chr_1 g10031 g10031.t1 TTS g10031.t1 6861730 6861730

Sequences

>g10031.t1 Gene=g10031 Length=1572
ATGTGGTATTTAGTAAATTTACCGGGAAATAAATTGAACGTGGCTGTTAAAACTGAAAAA
AATTCGATTGCCGCCGATTGTTTAAATAAAGTGTGTCATGATTTGGGGATTATTTGCGAG
ACAGATTATTTTGGTTTATTATATGCACCATCACCACACGATCATCATGATCATGATCAA
ATACACATCAAACAATGGATTAATTTAAGGAATCCTTTGGATAAAAGACATAAAGGCGAA
AGTCCAACATTACTTGAATTGCGCGTAAAATTTTGGGTACCCGCTCATCTAATTCTACAA
GAAAATGTTCGTGAGATATTTTACATGCAAGCACGACAGATGTTAATTGACAATGAAATT
CATCCAAGTGATTGGAAGCAAGCAGCACGAATGACAGCACTCATGGCACAAGCACAAGGA
GTAAAATTCATACCTGAATTGTTGACAGAAAATGGTCAAAAGGTTATCGCGGAATTTGGC
AAAAACATTCAACAAAATTTAAAGCGTGTCAAAAACAAATCAAGCGATAACGCGCATTAC
ATGATAAAGCGAAATTCATTTGATGAAATGAAAGTAGATAGTGATTGCGATAAAGAGTTC
CTACACTCATACGATAACCGGTACCTAGAGAGATTTATTATTGAGAATTATTTAGAGCAC
ATGACATTTCCGTGCTATGACAGTGACGAAGATGATGTTGATAATAACAATAGCAAAGAA
GAAACTGTTGTGCTTGAAGATGATGCTCAATTATCTAATTTCTTACTTAATATAGCTAGA
GAGCATCAGAAAATTAACAAAATTACGCAAGTTTCTGCAAAATATTGGCTTCTCGAAGAA
TTTTCAACACTCAAGGGCTTTGGTGAGGAAACATTTGAGGGAACTTTAATTTCGGAAAGT
GAATCAAAAGTTACACAACAGCGTAATGAAAAAATTAGAATTGCTGTAAATTCACAAGGT
CTTAATGTGAACAAACTAGAAAGTCATCAAAAATTTTCAATTCCATTTGCGGCAGTTGAA
TCTGCAAAATCTCTAAGACGGTGTTTTCACCTTTGCTATTTAAATGAAAACTATACTGAT
TCAAGTATGATCATCAAGTTCACATCACATCGTATTGCAGGAACTTTGTATCGTGCTTTA
ACAGAAAAGCATTCATTCTATAGCTGTGAGACTGTCCATAAGAATGTCGAGACACAATTT
ATTCGCGACTTAAAGGGTACAATTGTATCAATGTTCAATGAGGATACAGAATTAGGAAAA
AAATATGTTTTTGATATAAGACTAACGTTTAGAGAATTGTATGACAATTCAAGACGAATA
CTTCATGCCAAAGGTATTGATGTTTCGAAAAGGCCAAGTGTACAAGATGATATGGGTCAA
ACATCAACTTGTGAATTAGATAACAATAAGCGAATCGATATGACATGCTCAATTTGTATG
GACCAAAAAATTGATACTCTTTTCTTACCCTGTGCTCATTTATCATGTTGTAGGAATTGT
GCTGGCAAATGTGAAATTTGTCCTCTATGTCGTAAGAGTATAGCATCAACTTCCTTAGTA
TATTTTACATGA

>g10031.t1 Gene=g10031 Length=523
MWYLVNLPGNKLNVAVKTEKNSIAADCLNKVCHDLGIICETDYFGLLYAPSPHDHHDHDQ
IHIKQWINLRNPLDKRHKGESPTLLELRVKFWVPAHLILQENVREIFYMQARQMLIDNEI
HPSDWKQAARMTALMAQAQGVKFIPELLTENGQKVIAEFGKNIQQNLKRVKNKSSDNAHY
MIKRNSFDEMKVDSDCDKEFLHSYDNRYLERFIIENYLEHMTFPCYDSDEDDVDNNNSKE
ETVVLEDDAQLSNFLLNIAREHQKINKITQVSAKYWLLEEFSTLKGFGEETFEGTLISES
ESKVTQQRNEKIRIAVNSQGLNVNKLESHQKFSIPFAAVESAKSLRRCFHLCYLNENYTD
SSMIIKFTSHRIAGTLYRALTEKHSFYSCETVHKNVETQFIRDLKGTIVSMFNEDTELGK
KYVFDIRLTFRELYDNSRRILHAKGIDVSKRPSVQDDMGQTSTCELDNNKRIDMTCSICM
DQKIDTLFLPCAHLSCCRNCAGKCEICPLCRKSIASTSLVYFT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g10031.t1 CDD cd14473 FERM_B-lobe 104 178 0.0073448
12 g10031.t1 Gene3D G3DSA:3.10.20.90 - 5 90 0.0000000
13 g10031.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 452 522 0.0000000
4 g10031.t1 PANTHER PTHR23280:SF13 E3 UBIQUITIN-PROTEIN LIGASE MYLIP 1 523 0.0000000
5 g10031.t1 PANTHER PTHR23280 4.1 G PROTEIN 1 523 0.0000000
3 g10031.t1 Pfam PF09379 FERM N-terminal domain 14 75 0.0000004
1 g10031.t1 Pfam PF00373 FERM central domain 98 292 0.0000000
2 g10031.t1 Pfam PF13920 Zinc finger, C3HC4 type (RING finger) 473 516 0.0000000
15 g10031.t1 ProSiteProfiles PS50057 FERM domain profile. 1 391 26.9910000
14 g10031.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 476 511 10.7040000
11 g10031.t1 SMART SM00295 B41_5 6 292 0.0000320
10 g10031.t1 SMART SM01196 FERM_C_3 306 395 0.0000024
8 g10031.t1 SUPERFAMILY SSF54236 Ubiquitin-like 4 94 0.0000000
9 g10031.t1 SUPERFAMILY SSF47031 Second domain of FERM 88 180 0.0000030
6 g10031.t1 SUPERFAMILY SSF50729 PH domain-like 305 402 0.0000197
7 g10031.t1 SUPERFAMILY SSF57850 RING/U-box 469 515 0.0000012

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:0005856 cytoskeleton CC

KEGG

Orthology

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.

Raw TPM values