Special

GgaINT0116825 @ galGal4

Intron Retention

Gene
Description
T-cell lymphoma invasion and metastasis 1 [Source:HGNC Symbol;Acc:HGNC:11805]
Coordinates
chr1:103797709-103799707:-
Coord C1 exon
chr1:103799589-103799707
Coord A exon
chr1:103797818-103799588
Coord C2 exon
chr1:103797709-103797817
Length
1771 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
CGTGTGTTTGTGATTGGCAGGTT
3' ss Score
8.16
Exon sequences
Seq C1 exon
TGGCCATAAAAACAATGAACAAAGTTGCCAGCCATATTAACGAAATGCAAAAAATCCATGAAGAATATGGGGCAGTGTTTGACCAACTCATAGCAGAACAAACAGGAGAGAAAAAAGAG
Seq A exon
GTAACAAACAATTTTTAAATAAAATAAATAGGCTGTTATTTTGGTGCCTGTAGCGTGAATGTTAAATTTTACCAAATAGTTGCCTTTCCTTCTGTGTCACTGAAGTAATTCCTGTGCAAAGAGGTAAAACCCAATCCAGTTAAAAAAACTGTTTCTGTGTATACAGTTCACTGAGTAGGACCAATGTAAAGAAGTGCATTAATTCACTTTGAAGGTTGTGCTTGGGTCAAAATCTCAGTTCAACTTTTTAATGTCTGTATCTTGGCTCTCCTCTCTCAAGACAATCTCACCCCACCAGTCTGAATAGATGGATGTCCTGAGGCAAGTTTGTATTTATCTCTTTAATCACTTCAAAGAGATCAAAGTGAGATCCAGTGTGTGTGAGTAGCTGCTACTTCTGATTCAGAAAGTGTGTTAGTGGGCTTGATGTATGAGAGTCCTGGACTTCAGTCCAGATCTTGCAGAGTGCTTACTGAAACACCTGAAGGTTGAATATGCTCAGTCTTGGGTGCAGAAACCTGTGGAAGATGTGTTGAAGTTTCAAACTGAGACCTGGATCACTCATTTACTGAGTAGAGTGTGGGCCTTCAGCCCAACAGTGTCATGAAGGAGAGTAGTGTGAAGTAATAGGCAAGGTCAGGAGAGACTTGAGGAAAAGGTGTAGACATGCTGAAGCTGGAGAAACACGACGATAAGAAGTAACGGTAGTAGGGTTTTGCCAACCACTGGGATGAAGATCAAGCCAAAGAGCTGCTGTGCAAATACAGGACACAGGTGGTTTGGGATTGAATGAATGGTCCTGGGGAAGTTTTGGGTGAGCAACTTCTACAACAGCAGCGGGGAGAAGCAAGTGGTGGAAGAGAGCAGAGACCAGGTGACCTTGGCAAAGCTGTGCTGATGCTGGCAAAGAGAAGTTGGGAGAATGGGTCAGGACTTCTGTTGACAGAACAGCTGTGGCTTGGTGTTAATTTGGGAGAGGAGACAACAAACATATCTTAGTGTTGCTCTTGTTATCAGGGAGAGCTCAGGTTGTTTTGCTCACGTTATCTGTGATATCCTTTTGCAAAAGCCAAATTTCACTGAGAGAAGGGTGGAGGAATGGTGTAAGATGGCCCCAAGACTGGAGGTCACCCTTGAATTATCACTTTGGGAGAAGTCAAAGTAAAAGATCTGGTTGCTGCAATAGCACTAGTATGCATATCCCAACAGTCATTAAGAACTCTGTTCTTAGTCCATTCTCATCAATATGATTTTCACAAGTGAACCTTTGGGGGAAATCACGAACCATGGCAAATATGGGGGGGACGTTGCTGTGACTACTTCACCTGGTGCTATCTTTGAACTTCACTCCAAACCTCATGTGTGTGAGTGGTGGGATGGAGTATGCTTAGATCTTCAAACAAAATACCACGAAGCTGGTAAGAAGAAGGATGGCAAAGGAGCAAACAAAAACACAAGGGAAAGAGTTTATGTTTTTGTCATTTTGCCAGCCCTGGCCTCCTACAAAATTTTGAGAGCCAGGCTGAGTCTGGCTTCTTCTTATTTATGCCCTCCAATTAAAGATTTACACACGTCTATTGCCATCTGTCAGTCTGTTTGCACACACTTGCAGTCATCTGGTTAAATAACCTATTCCAAAAATTTACTTGTGTTTTGTTTGTTTGTTTGTTTTAGATTTAAGTCCAGGAAAGTTTTCTTGAACTGGAGTTCAAGAAAGAAAAATTTGGACTGAAATACACTGTTTCTTTGTGCGTGTGTTTGTGATTGGCAG
Seq C2 exon
GTTGCAGACCTTTCCATGGGGGATTTGCTCTTGCATAACACAGTGATATGGCTTAATCCTCCTGCTTCACTGGGGAAATGGAAGAAGGAACCTGAGCTGGCAGCATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015842:ENSGALT00000025542:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):

C1:
PF0062115=RhoGEF=PD(7.4=35.0)
A:
NA
C2:
PF0016924=PH=PU(23.5=83.8)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
TAAAAACAATGAACAAAGTTGCCAGC
R:
CAAATGCTGCCAGCTCAGGTT
Band lengths:
222-1993
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]