Sequence
atgc intronic sequence ATGC exonic sequencegtaattcgtgtttgctctttcaactataaataccatgctagtaatttgctttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30000.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G28910.2 (Glycine max), 3'ss of exon 2
gtaattcgtgtttgctctttcaactataaataccatgctagtaatttgctttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT
| ||| | ||| | | | | ||| || || |||| || || || | | | | | | || ||||||||||| | ||||| ||| ||| || ||||| || |||||||||||||||| || ||||||||||| ||||| || || ||||||||| ||||||
---caccccaattgttttttt--ttgtcacctttaggcttgtgtcttcttttcttttctcgtcattttctactgacttttagatatctctaataactaaatgcagCCCTCATTCTGGTGAATTTAGTGGAGAAAATATTAGACTGGGATCTCGTGGTGACAGTTACTATGAGTACTTAATCAAAGTATGGCTTCAGAGTGGAGCT
upper sequence: AT1G30000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G10130.1 (Glycine max), 3'ss of exon 2
gtaattcgtgtttgctctttcaactataaataccatgctagtaatttgctttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT
| ||| | ||| ||| | | ||| || || |||| || || || | || | | | | || ||||||||||| | ||||| ||| ||| || ||||| || ||||||||||||| || || ||||||||||| ||||| || || ||||||||| |||||
----accccaattgtttttttt-ttatcacctttaggcttgtgtctttttttcttttctcatcattttctactgacatttagatatctctaataactaaatgcagCCCTCATTCTGGTGAGTTTAGTGGAGAAAATATTAGACTGGGATCTCGTGGGGACAGTTACTATGAGTACTTAATCAAAGTATGGCTTCAGAGTGGAGCA
upper sequence: AT1G30000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0003g03280.t01 (Vitis vinifera), 3'ss of exon 2
-gtaattcgtgtttgctctttcaactataaataccatgctagtaatttgctttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT
| | | || ||||| || ||| || | | || | || | | ||| | || | ||| | | |||||| | ||||||||||| | ||||| ||| ||| || |||||| | |||||||| |||||||| |||||||||||||| |||||||| |||||||||||||| ||||||
tttctcttggaaatgttcttttgtagattaatgtaat--ttatgatata---tctggggatagtaggggtattagtgttttgatatcatctttctat-taatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT
atctgac putative branch site (score: 3)
tttctacct putative PPT
ttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcgtgtttgctctttcaactataaataccatgctagtaatttgctttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT