Sequence
atgc intronic sequence ATGC exonic sequencegtacacaacgcatttctatatataccattcttcaatctaaagctgattgattgtcatagtttaagaaatgttgtgtggtgttttggcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27910.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G179814_T01 (Zea mays), 3'ss of exon 3
------gtacacaacgcatttctatatataccattcttcaatctaaagctgattgattgtcatagtttaagaa--atgttgtgtggtgttttgg---cagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
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ggattggcttaggacaagaccaaaaacggcctatatttcgaaacggggtcatgaacacacaactctcgactgatcatgttatttgctttgttaattccagGTATGACTACCTGTTCGATCCAGACGAGGCCGATGAACGCAAAGTGCCATGCCTTTGTCAGACTGCTAACTGCCGGAAATTCATGAATTAGTTCGCTTAG
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 23
gtaca---caacgcatttctatatatac-cattcttcaatctaaagctgattgattgtcatagtttaagaaatgttgtgtggtgttttggcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
||| | | | | | | | | | ||| | || || | | |||||| | | ||||| | | |||| ||||||||||| ||||| |||||||| || ||| |||||||| ||| || |||||| |||||||||| || |||||| ||||||||||||||||| | ||
gtatgtctctgtgtgtgtgcacgcgtgcgtgcgcatgtatcagtatgtgcatgttctttatagttgatgctg-gttgttttg-gtttgggcagGTATGACTACTTGTTTGATCCTGATGAGCCAGAGGAAAACAAAGTCCCATGCCTATGTAAAGCTCCAAACTGCCGGAAATTCATGAATTAGGAAGGATTA
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 23
gtacacaacgcatttctatatataccattcttcaatctaaagctgattgattgtcatagtttaagaaatgttgtgtggtgttttggcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
||| | | | | | | | | | | | | | || || | |||||| | | ||||| | | |||| ||||||||||| ||||| |||||||| || ||| |||||||| ||| || || ||| |||||||||| || |||||| |||||| |||||||||| | ||
gtatgtctctc-tctttgtgtgtgt-gtgcatgtgttgtagcatgcatgttctgtatagttgatgctg-gttgttttg-gtttgggcagGTATGACTACTTGTTTGATCCTGATGAGCCAGAGGAAAACAAAGTCCCGTGCCTATGTAAAGCTCCAAACTGCCGGAAATACATGAATTAGGAAGGATTA
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 14
----------------------------------------------------------------------------gtacacaacgcatt-tctatatataccattcttcaatctaaagctgattgattg---------tcatagtttaagaaatgttgtgtggtgttttg----------gcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
| | || |||| || | ||| | | | | | |||| |||| || |||||| | || | | || ||| |||||||||| ||||| |||||||| || ||| |||| ||| | || || || || ||||||||||| | |||||| ||||||||||||||||| || |
gtgagtctaactgcttatttctgtagtgtttggtccaggttttttctagtttttcttctacttaaaaagagaagttgggccaaatacattgtccaaata-attaaagtctattagaaagtgtattgtttaggcatttctctttagttttcagtttttttttttctgacttgattgtaactggcagGTATGACTACTTGTTTGATCCTGATGAGCCAGATGAATTTAAAGTCCCTTGTTTATGTAAAGCATCAAACTGCCGGAAATTCATGAATTAGGATTTATTC
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA19G17460.2 (Glycine max), 3'ss of exon 14
gtacacaacgcatttctatatataccattcttcaatctaaagctgattgattgtcat--agtttaagaaatgttgtgtggtgttttg----------gcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
|||| || | || | | ||| | | || | | | ||| | ||||| | || | | || ||| |||||||||| ||||| |||||||| || ||| |||| ||| | || || || || ||||||||||| | |||||| ||||||||||||||||| || |
-tacattgtccaaataattaaagtctattagaaagtgtattgtttaggcatttctctttagttttcagtttttttttttctgacttgattgtaactggcagGTATGACTACTTGTTTGATCCTGATGAGCCAGATGAATTTAAAGTCCCTTGTTTATGTAAAGCATCAAACTGCCGGAAATTCATGAATTAGGATTTATTC
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 23
-----gtacacaa---cgcatttctatatataccattcttcaatctaaagctgattgattgtcatagtttaagaaatgttgtgtggtgttttg---gcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGA-ATAGAAAG
| |||| | | ||| | | | | | | | || || || | | | | ||| ||| ||||||| || |||||||||| ||||| |||||||| || ||| | || ||| |||||| || || || |||||||| || |||||||| ||||||||||||||| || | |
agatttcaaacaaattcagacttcagataaaagaaaacatacaccggccactacatgtttagagtgttgtgataaactatgtatggtgttgtgtttgcagGTATGACTACTTGTTTGATCCCGATGAGCCGGACGAATGCAAGGTCCCCTGTTTGTGTAAAGCTCCAAACTGCAGAAAATTCATGAATTAGGTATTTACA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctaaagctgattgattgtcatagtttaagaaatgttgtgtggtgttttggcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
atagtttaagaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacaacgcatttctatatataccattcttcaatctaaagctgattgattgtcatagtttaagaaatgttgtgtggtgttttggcagGTATGATTACTTATTTGATCCAGACGAGGCAGAGGAACTCAAGGTGCCATGCTTATGTAAAGCCCCTAACTGCAGGAAATTCATGAATTAGAATAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG