Sequence
atgc intronic sequence ATGC exonic sequencegtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgtgtgatcatgtaaaggaaagaggttttttgagatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01830.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G125943_T01 (Zea mays), 3'ss of exon 3
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgtgtgatcatgtaaaggaaagaggttttttgagatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
||| | || || || || | | | ||| || ||| || ||| | | | | || | | | || || ||| |||| | ||| || |||||||| ||||||||||||||||| || || |||||||| || | | |||||||| || || | || || ||| |||| |||||| ||||
--------------------------------------------------------gatcatgcaggtt--ataatcattgca-gcttgtctcaatttaatcaaa----------tgatactctatgcttatctaattttcaagagaataatt--tgctgtgtgct----cccagATATCTTGGTGGAGCGTTTGATGTGGAGTCACTTGTGGAGAATTTGCTGAGCAAACTTGCTGGCAATCAGGATATTGTGGTGAATGTCTATGATGTCACA
upper sequence: AT2G01830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G34310.1 (Glycine max), 3'ss of exon 3
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgtgtgatc--atgtaaaggaaagaggttttttg-agatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
| ||| || | || | || | || ||| || | |||| | | | ||| || | ||||| | |||| ||| | |||| |||| ||| || |||| || | |||||||| ||||| || || ||||||||||||||||| ||||||||| |||||||||| | ||| | || |||||||||||
----------------------------------------------------------------------gaggatgagtctgtgactttggttcaatctaatggctttatgtttcccggaaaattctttatgccatcatgtgttcaataaacatt------ttaattggaaa--cagATATGTTGGAGGATCCTTTGATGTTGAGTCCCTCGTGGAGAATTTACTTGGTCAACTTGCTGGTCACCAAGCAATTTTGGTGAACGTATATGATATCACA
upper sequence: AT2G01830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05370.1 (Glycine max), 3'ss of exon 3
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgtgtgatc--atgtaaaggaaagaggttttttg-agatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
||||| || | | | || | || ||| || | |||| | | ||| || | ||||| | |||| ||| | |||| ||| |||| || |||| || | ||||| || ||||| || || ||||||||||||||||| ||||||||| |||||||||| | ||| | || |||||||||||
----------------------------------------------------------------------gatgatgagtctgtaactatggttcaatctaatggctctatgtttcccataaaattctttatgccatcatgtgttcaataaacatt------ttaattggaa--gcagATATGTTGGAGGATCCTTTGACGTTGAGTCCCTCGTGGAGAATTTACTTGGTCAACTTGCTGGTCACCAAGCAATTTTGGTGAACGTATATGATATCACA
upper sequence: AT2G01830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G27540.1 (Glycine max), 3'ss of exon 3
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgt-gtgatcatgtaaaggaaagaggttttttgagatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
|| | || | | | |||| | | ||| | | | | | || || | || ||| | | |||| || | |||| || ||| || |||| || | |||||||| ||||| || || ||||||||||||| || |||| ||||||||||||||| | ||| |||| |||||||| ||
---------------------------------------------------------atcgacaagcctctttaccttgtttcaatcttgtggctttatgtttacactaagcttcttagtgtcctaa----------tgtattgaataaa--------tttctaattgacat-cagATATGTTGGAGGATCCTTTGATGTTGAGTCCCTTGTAAAGAATTTACTTGGGCAACTTGATGGTAACCAAGCAATTTTGGTGAATGTATATGATATTACA
upper sequence: AT2G01830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G09550.1 (Glycine max), 3'ss of exon 3
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatt-tcatgattggtttatgtgtgtgatcatgtaaaggaaagaggttttttgagatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
|| | || | | | |||||| | |||| | | | | || || | || ||| | | |||| || | |||| || ||| || |||| || | |||||||| ||||| || || ||||||||||||| || |||| ||||||||||||||| | ||| |||| |||||| | ||
---------------------------------------------------------atcgacaagcctcttaaccttggttcaatcttgtggctttatgtttactgtaagcttcttagtgtcctaa----------tgtattgaataaa--------tttctaattgacat-cagATATGTTGGAGGATCCTTTGATGTTGAGTCCCTTGTAAAGAATTTACTTGGGCAACTTGATGGTAACCAAGCAATTTTGGTGAATGTATATGATGTTACA
upper sequence: AT2G01830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g06190.t01 (Vitis vinifera), 3'ss of exon 3
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgtgtgatcatgtaaaggaaagaggttttttgagatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
|||| ||||| ||| | ||| ||||| || |||| | | | ||| ||| || || ||||| | || ||| ||| |||||| |||| ||||||||||| || |||||||||||||| || || |||||||||||||| || |||||||| || || ||||| | ||| |||| |||||| | ||
----------------------------------------------tgtatgccttcatttt---aattcaacttcaattttgtgtgtttgttcatatggaag------------------ttctggatgcattcatgggtaaaatgaaaatt-----ctga--ttgaaa-gcagATACCTTGGTGGAGCCTTTGATGTGGAGTCCCTGGTGGAGAATTTACTTGGGCAACTTGCTGGGAATCAGGCAATTTTGGTGAATGTCTATGATGTAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
gattgat putative branch site (score: 4)
aatttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagttcccatctgattactggagcaaacttttgcttgtgatcatgtaaaaagagattttcgagatttcatgattggtttatgtgtgtgatcatgtaaaggaaagaggttttttgagatttcaagattggtttgtgtgtaaagtaaagattgatgcttgaatttgaaatgcagGTACCTTGGTGGTGCGTTTGATGTGGAGTCTCTAGTCGAGAATTTACTTGGTCAGCTTGCTGGTAACCAAGCAATAGTTGTGCATGTGTATGATATCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA