Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgcgaaatccttttgtgcctcatcacatttcattagtatcatgtgatcatgtcaaaagtctagctaaaccatggctaatacttcgtggctttgaatagtttaagacattttttctttctgttttgtcatctattggatcgctttgcaaatctttatagactaacatttaaaagaactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G13020.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G10820.2 (Glycine max), 3'ss of exon 9
gtatgtttgcgaaatccttttgtgcctcatcacatttcattagtatcatgtgatcatgtcaaaagtctagctaaaccatggctaatacttcgtggctttgaatagtttaagacattttttctttctgttttgtcatctattggatcgctttgcaaatctttatagactaacatttaaaagaactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG
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----------------------------------------------------------------------------tgtgatgaa-acttgtttgcc----attatttatgccataacgc------agatgatattatgcttgctttcttcttaaggtggtgaataacaa-atataaattatttgcagACATGTGGGCAGTTGGTGCCATATTAGCTGAGCTTTTTACTTTGACCCCTATATTTCCTGGTGAAAG
upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G21610.2 (Glycine max), 3'ss of exon 8
gtatgtttgcgaaatccttttgtgcctcatcacatttcattagtatcatgtgatcatgtcaaaagtctagctaaaccatggctaatacttcgtggctttgaatagtttaagacattttttctttctgttttgtcatctattggatcgctttgcaaatctttatagactaacatttaaaag--aactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG
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-----------------------------------------------------------------------------atggtgaa-acttgtttgccctta----tttatggtgtaactc------agatgatattatgcttgctttcttcttaagg--tggtgaaataacaaatagaaattatttgcagACATGTGGGCAGTTGGTGCTATATTAGCTGAGCTTTTTACTTTGACCCCCATATTTCCTGGTGAAAG
upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtttgcgaaatccttttgtgcctcatcacatttcattagtatcatgtgatcatgtcaaaagtctagctaaaccatggctaatacttcgtggctttgaatagtttaagacattttttctttctgttttgtcatctattggatcgctttgcaaatctttatagactaacatttaaaagaactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG
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-------------------------------------------------------------------------------------tggtttg-agctctaattgattcatgttaaattgctcatttggagattcatttagt--attggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctattggatcgctttgcaaatctttatagactaacatttaaaagaactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG
gactaac putative branch site (score: 1)
tttatagactaacatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgcgaaatccttttgtgcctcatcacatttcattagtatcatgtgatcatgtcaaaagtctagctaaaccatggctaatacttcgtggctttgaatagtttaagacattttttctttctgttttgtcatctattggatcgctttgcaaatctttatagactaacatttaaaagaactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT