Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcacactttcaatataatgttaaatgcaattggatttgaaacaaagaatcaattgtttaaacttgattacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25690.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25690.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 3
-----------------------------------------gtaagttcacactttcaatataatgttaaatgcaattggatt--tgaaacaaagaatcaattgtttaaac-------ttgattacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
| | | | | | | | ||| | || | |||| | | | | || | |||| || || ||||| ||||||||||||||||||||||| |||||||| |||| |||||| ||| |||||||| | ||| | || || ||| | | || || |
gtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattcccttagtccattagtaatt-caggtagattattatgaggactgactttttatataaaaaaatggatttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGTTTTGTAAATATCGACGATGTTGTTGCATTTG
upper sequence: AT3G25690.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g01449.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------gtaagttcacactttcaatataatgttaaatgcaattggatttgaaacaaagaatcaattgtt---taaac-------ttgattacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
| | | | || | | | || ||| | || | |||| | | || | | || || |||| || || ||||| |||| |||||||||||||||||| |||||||| |||| |||||| ||| |||||||| || ||| | || || || | | || || |
gtaagttattcaagatgatgctacctttcagaaatatatactactgaattcctttagtccactgctaatt-caggtagatt-attatgaggacttactttttatataaaaaaatggatttgtttcagGTCAAAGTGGATGTGGAGACACAAGGAGACTTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTG
upper sequence: AT3G25690.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------gtaagttcacactttcaat--ataatgttaaat-gcaattggatttgaa----acaaagaatcaattgttt-----aaacttga----ttacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
| ||||| |||| | ||| ||||| ||| | | || |||| || ||||| ||| ||||| |||| || | ||||||||||| ||||||||||||||||| || ||||| |||| |||||| ||| |||||||| | || | || || ||| | | || || |
gtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttc-cactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaatgctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
upper sequence: AT3G25690.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------gtaagttcacactttcaatataatgttaaat---gcaattggatttgaa--acaaagaat--caattgttt-----aaacttga----ttacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
| ||||| |||| | ||| | ||||| | ||| ||||| || | || | | ||| ||||| |||| || || ||||||||||| ||||||||||||||||| || ||||| | || |||||| ||| |||||||| | |||| | || || || | | || || |
gtaagtattttctgctggcaccatcttgaacaaaaatcctgtgaaatttatgagttc-cactattaatgcataattaaaactagtaatcagatttcaataatgaaaagtgacaaatgttttataaaaacatggaatgtttcagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAATCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTCATAAATATTGATGACGTTGTTGCATTTG
upper sequence: AT3G25690.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g02860.t01 (Vitis vinifera), 3'ss of exon 4
---------------------gtaagttcacactttcaatataatgttaaatgcaattggatttgaaac--aaagaatc----aattgtttaaacttgattacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
| || | | ||| | | | | | | ||| || ||| || || | ||| || ||||| ||||| |||||||| || ||||| || ||||| ||||| || ||||||||||| |||||| |||| || ||| | ||||||||||| |||| || |
gtacgttaaattttcccatacatccatttatcttctcaggcaggttgtttgggtgttcatttctcaaatttaacaaatattgaaactggatggactggaac-cagGTGAAAGCTGATGTGGAAACTCAAGGTGATTTTGTCCAGTCATTGGCAACTGAAGTTCGAGCTGCTTCCTTTACCAAAATAGAAGATCTGGTGGCCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaaatgcaattggatttgaaacaaagaatcaattgtttaaacttgattacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
acttgat putative branch site (score: 5)
aatcaattgtttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcacactttcaatataatgttaaatgcaattggatttgaaacaaagaatcaattgtttaaacttgattacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT