Sequence
atgc intronic sequence ATGC exonic sequence...cattacatgtagtttttgttgttgattcacaagaatgtcttactggttcattagatattactataatgaattttattctggaaacatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA
Basic information
species | Glycine max |
transcript | GLYMA11G12280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 5
cattacatgtagtttttgttgttgattcacaagaatgtcttactggttcattagatattactataatgaattttattctg-gaaacatgtta-tattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA------------
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cagcagatgaggcataagtgaata--ttgttagattttagtttcttcacatgagctcccatgcttaccactttggtacaatgatacatttttctaccttcagGTTTTACAAGAGAAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAG
upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 5
cattacatgtagtttttgttgttgattca-caagaatgtcttactggttcattagatattactataatgaatt--ttat-tctggaa---acatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA------------
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--------------------gtaaattaagccagagtgtctctgctatgctctaaa-actatgcaaatgaattggttatatctatgatagactttatacatgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
cattacatgtagtttttgttgttgattcacaagaatgtcttactggttcattagat--attac-tataatgaattttattctggaaacatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA------------------------------------
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-attat-tgtc-tcagagaaatttatttacaagtccttaatattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 6
cattacatgtagtttttgttgttgattcacaagaatgtcttactg-gttcattagatattactat---aatgaattttattctggaa-acatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA------------
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---tccaaata--ccttggtcaagattctcttctcttccatccagtatagatgtgaaattcagatctaagtgtacatcattctaaaatgtttgtattgttaacagGTCCTACAGGAAAAGGGAATTCATATATGGGATGGCAATGCATCCAGGGACTACCTTGATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcattagatattactataatgaattttattctggaaacatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA
ttagatattactataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattacatgtagtttttgttgttgattcacaagaatgtcttactggttcattagatattactataatgaattttattctggaaacatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - acatgta
- - - - - - - - -gttgttg
- - - - - - - - - - - - attcaca
- - - - - - - - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtt