Sequence
atgc intronic sequence ATGC exonic sequence...ttgatccttgtacctaaattacatccctatgctagtttctcatggcaatatttttggcaagcttcagtcatctaactactttgtacattttgtactgtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50590.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA05G10590.1 (Glycine max), 3'ss of exon 22
ttgatccttgtacctaaattacatccctatgctagtt-tctcatggcaatatttttggcaagcttcagtcatctaactactttgtacattttgtac----tgtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
| | | | | | | ||| | | | | || | ||||| | | | | | |||||| ||| || || | ||||||||| ||||| ||||||||||| |||||||| |||| ||| |||| || ||||| ||||| |||||||||||||| || || ||||| |||
--agctcccacaattga--tgctttggcatgtggatgatactgtagttatttgaatggcatgatctacaagtttg-ttacttttctaattgaaggtcacttgcagGTTTGGTCAATTTGATAGTGCAAAGGAAACATTTGAAGTTATAGCAGACAATGAAAGTATGCTTGATCTGTTTATATGCCACCTTAATCCCAGTGCCATG
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA17G20310.1 (Glycine max), 3'ss of exon 22
-----------ttgatcctt--gtacctaaattacatccctatgctagtttctcatggcaatatttttggcaagcttcagtcatctaactactttgtacattttgtactgtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
||||| ||| | | | || | | || | | ||| |||||| || | |||| || || || | ||| || | | || || | ||||||||| ||||| ||||||||||| |||||||| |||| || ||||| || ||||| ||||| |||||||||||||| || || ||||| |||
agctcccacaattgatgctttggcatgtggatgata---ctgtagttatttga-atggcatgatct---acaagttt--gttatttttctaattgaaagtcact----tgcagGTTTGGTCAATTTGATAGTGCAAAGGAAACATTTGAAGTTATAGCAGATTATGAAAGTATGCTTGATCTGTTTATATGCCACCTTAATCCCAGTGCCATG
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 22
-ttgatccttgtacctaaattacatccctatgctagtttc-tcatggcaatatttttggcaagcttcagtcatctaactactttgtacattttgtact-gtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
| | || || | | || ||| || ||| || | |||| || || | || | ||| || || | |||| | || | ||| || || ||||| ||||| ||||| |||||||| | | || || | |||||||| ||||| |||||||||||||| || ||||||||||||
actatttgatgagcc---agtgtataatgatgatactttagtcctttgaatagttatgtgatttaaaggtttgttcactttttgttatttaagatacttgcagGTTTGGCCAGTTTGATAGAGCAAAAGAAACCTTTGAAGTTACTGCAGATTACAAAAGCATGCTTGATCTATTTATATGCCACCTTAATCCTAGTGCTATG
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: PP1S47_192V6.1 (Physcomitrella patens), 3'ss of exon 21
-------ttgatccttgtacctaaattacatccctatgctagtttctcatggcaatatttttggcaagcttcagtcatctaactactttgtacattttgtactgtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
| | || || || | ||| | ||| || |||| | ||| | | | | | | | ||| ||| | | | | ||||| ||||| |||||||| | ||||| ||||||||||| || | | || ||||| |||||||| ||||||||||||||||| | || || ||||| ||
gggagtgtaggtcgttttaa--agtttatttgtttat-ttatcttcttttaacaa--ctctaatcctctgtgtgcctgacatctattttattgactcgga--tgtagTTATGGACAATTCGACATGGCAAAAGAAACTTTTGAGGTCGTGGCAGATTATGAAAGCATGCTGGATCTTTTTATATGCCATTTGAATCCAAGTGCGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatttttggcaagcttcagtcatctaactactttgtacattttgtactgtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
atctaac putative branch site (score: 2)
tacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgatccttgtacctaaattacatccctatgctagtttctcatggcaatatttttggcaagcttcagtcatctaactactttgtacattttgtactgtagATATGGTCAATTCGATAGCGCAAAGGAAACTTTTGAAGTAATAGGCGACTATGAGAGCATGCTAGATCTTTTTATATGCCACCTCAACCCTAGTGCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - -acctaaa
- - - - - - - - - - - atcccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctaa