Sequence
atgc intronic sequence ATGC exonic sequence...ttaaattctgtatcaatatcgtcaaaagatcaaatctttattagttgttttctttcccctctttccaaaaaatctctaatttgtgtgttttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 1
ttaaattctgtatcaatatcgtcaaaagatcaaatctttattagttgttttctttcccctctttccaaaaaatctctaatttgtgtgttttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
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---------gtatgtatat-accaagttaccaactctcacattaccatgctatttgtgtttttttggtttgcttatttatgtgtgaatgt-gcaatgcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTGAAATTTGGTTTTCCCATGGCATTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
upper sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G37420.1 (Glycine max), 3'ss of exon 1
-ttaaattctgtatcaatatcgtcaaaagatc--aaatctttattagttgttttctttcccctctttccaaaaaatctctaatttgtgtgttttgttgat----tagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
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gtatgataatataataatattaatacaacattcttagtctcagtctcagtttttgtgttctctggcttgtgcacatggcttatttctgcattgaatgtacaatgcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTCAAGTTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCGTGGAGTGTTATTGAGT
upper sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
ttaaattctgtatcaatatcgtcaaaagatcaaatctt-tattagt-tgttttctttcccctctttccaaaaaatctctaatttgtgtgt---tttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
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------------------gtatgcatataccaactctcacattaccatgttttctggtttttgtttttggt---ttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
upper sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G40030.1 (Glycine max), 3'ss of exon 2
ttaaattctgtatcaatatcgtcaaaagatcaaatctttattagttgttttctttcccctctttccaaaaaatctctaatttgtgtgttttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
|||||||||||||| |||| || |||||| |||| ||||| || || ||||| ||||| ||||| |||||||| ||||
-------------------------------------------------------------------------------------------------------------gttggagggtactacgatgttggggacaatgtcaagTTTGGGTTTCCCATGGCCTTCACCACCACCATGCTTTCGTGGA------------
upper sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
ttaaattctgtatcaatatcgtcaaaagatcaaatcttt--attagttgttttc--tttcccctctttccaaaaaatctct---aatttgtgtgttttgttgat----tagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
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-----gtatgtgtaaatgt----gtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttctttcccctctttccaaaaaatctctaatttgtgtgttttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
ctctaat putative branch site (score: 3)
ttttgtt putative PPT
aaaaaatctctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaattctgtatcaatatcgtcaaaagatcaaatctttattagttgttttctttcccctctttccaaaaaatctctaatttgtgtgttttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - caaaaga
- - - - - - - - - - - - - - -tcaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat