Sequence
atgc intronic sequence ATGC exonic sequence...agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgattgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54590.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G093858_T01 (Zea mays), 3'ss of exon 2
agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgattgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT-----------------------------------------
||| | || | | ||| | | | | || | || || | || ||| | ||||| | |||||||| || | |||||||| || ||| ||||||||||||| || || |||||||||||||| | |||||| |||| ||| | |||||
--------------------------ttggcttagaaccgtacatgctcttgctgagctccat---gattctgtctcataatctct------------agggagctacagaaagctacaagcaatttcacaacattgttagGCCAAGGAGCCTTCGGCCCTGTCTACAAAGCAGACATGTCTTCTGGCGAGGTACTGGCTGTCAAAGTGCTGTCGAACAATTCCAGGCAAGGTGAAAAGGA
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G093858_T02 (Zea mays), 3'ss of exon 2
agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgattg-cttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
| | | | | ||| || | || | | || | | || || | | ||| | | | || || ||||| | |||||||| || | |||||||| || ||| ||||||||||||| || || |||||||||||||| | |||||| |||| ||| | |||||
-accgctcagatataatcaaatccttgcggcccttctaatggttggcttagaaccgtacatgctcttgctgagctccatgattctgtctcataatctctagGGAGCTACAGAAAGCTACAAGCAATTTCACAACATTGTTAGGCCAAGGAGCCTTCGGCCCTGTCTACAAAGCAGACATGTCTTCTGGCGAGGTACTGGCT
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G16650.1 (Glycine max), 3'ss of exon 1
--agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgat-tgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
||| || || | || ||| || | | || || | || || ||| ||||| | | |||||||||||||||||||| || || ||||||||| || | ||||| ||||| |||||||| ||||| || |||||||| |||||||||||||||| || ||
actacagattgtttctaagagtgaaatccaaaatgattgaactctatgaaccgactgcatt---tttcattctttccattgaatcttttaagttatgcttcagGGATTTGCAGAAGGCAACACATAATTTCACCACGGTCATAGGACAAGGTGCATTTGGTCCTGTTTATAAAGCTCAGATGTCTACTGGTGAGACTGTTGCA
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G36140.2 (Glycine max), 3'ss of exon 2
----agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgattgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
|||| | || | ||| | | | | | | || |||| || | || | ||| || || | ||| || ||||||||||||||||| || || || | |||||| || || | ||||| ||||| |||||||| ||||| || |||||||| ||||||||||| |||| |||||
atcaagtttac-aatagtttgaaaacagaacatcttgtttcatgtcatttatctctttcttttttctttc-tttctgtttaatacttttttctg--tgcttcagGGATTTGCAAAAGGCAACATATAATTTTACAACACTCATAGGGCAAGGTGCATTTGGTCCTGTATATAAAGCTCAGATGTCTACTGGCGAGACTGTGGCA
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G34410.1 (Glycine max), 3'ss of exon 2
--agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgattgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
|||| | || | ||| | | ||| | |||| | |||| || ||| || ||| || ||||||||||||||||| || || || | |||||| || || | ||||| ||||| |||||||| ||||| || |||||||| ||||||||||| |||| || ||
caagtttac-aatagctcgaacacaacaacttct-tgattgatcatgtcatttatctctttatttttttctttctgtttacttctttttgtctatgcttcagGGATTTGCAAAAGGCAACATATAATTTTACAACACTCATAGGACAAGGCGCATTTGGTCCTGTATATAAAGCTCAGATGTCTACTGGCGAGACTGTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcattcttggggttatattccgtttttgacatatggtctttggtgattgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
ttttgac putative branch site (score: 3)
ttgcttc putative PPT
ttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttcattaaaaaggggaatgctgttgtggatatgagaaggtcttgcattcttggggttatattccgtttttgacatatggtctttggtgattgcttcagGGATTTGCAGAAAGCGACGTGTAATTTCACGACTTTGATAGGCCAAGGAGCATTTGGACCTGTCTACAAAGCTCAAATGTCTACTGGTGAGATCGTGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - -attaaaa