Sequence
atgc intronic sequence ATGC exonic sequencegtgagttccaataaattctctattaaacaatttatttcatctctttcttctttcttgtgtatttaattcccttctgaaacgttatcattctctttatatttaaatttgtattaatatgaagtaaattgtttgttatgttcagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
--------------------gtgagttc--caataaattct-ctatta--aacaatttattt-----catctctttcttctttcttgtgtatttaatt-cccttctgaaacgttatcattctctttatatttaaat--ttgtattaat-atgaagtaaatt-------------gtttgttatgtt-cagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG
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gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
upper sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
gtgagttccaataaattctctattaaacaatttatttcatctctttcttctttcttgtgtatttaattcccttctgaaacgttatcattctctttatatttaaatttgtattaatatgaagtaaattgtttgttatgtt-cagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG
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---------------------------------------ttgattgcgcatttcctagat-tcagattcttctctaggata--atcattttagtcaaaaaatgactttt-ttgttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
upper sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttccaataaattctctattaaacaatttatttcatctctttcttctttcttgtgtatttaattcccttctgaaacgttatcattctctttatatttaaatttgtattaat----atgaagtaaattgtttgttatgttcagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG
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------gtgagtaggatctcatctcgtggtcttgtcctgaatcatgatttttcactgttgaataaaaga--ttctgatattccttcaagttttagat-tctcattttggatcaatttttatttatttatttattttttgtttgcagGTGGGTATGATAAGGAAGAGAAGGCAGCTAGAGCTTATGATCTCGCCGCTCTTAAGTACTGGGGTCCGACCACCACCACTAACTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctttatatttaaatttgtattaatatgaagtaaattgtttgttatgttcagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG
tattaat putative branch site (score: 2)
tttatatttaaatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttccaataaattctctattaaacaatttatttcatctctttcttctttcttgtgtatttaattcccttctgaaacgttatcattctctttatatttaaatttgtattaatatgaagtaaattgtttgttatgttcagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC