Sequence
atgc intronic sequence ATGC exonic sequencegttgaatcaatttaaaatttctgacatatggattcctgttacttttaccaattatatgtcattctttagttctaagctgtactgcaagtcagtctggaactttatccacactaaaacttatcctatcgagtaattgtttttacacttttagACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25350.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 11
gttgaatcaatttaaaatttctgacatatggattcctgttacttttaccaattatatgtcattctttagttctaagctgtactgcaagtcagtctggaactttatccacactaaaacttatcctatcgagtaattgtttttacactttt---agACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
| ||||| || | | ||| || || | ||| || || ||| || | || | | | || | | | | | | || | || |||| || || || || || || ||||| || ||||||||||| || || |||||||| ||||| ||||||||||| || ||||| ||||| || |||||||
------------------------------gtttcctccagctctcttttttattatttcgatcc--aacagtaattgaagttgt--gtggagctgttacatcatgcccttgagaaataaaatgtgcacatgctgactggtatatgcttgccagACCGCAGAAGAAATCAAGGAATACAGGGAAAAGAAAATGAATAGTCCATGGAGGGATAGACCCATTGAAGAATCACTGAAACTATTTGAAGACATGAGAC
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 12
gttgaatcaatttaaaatttctgacatatggattcctgttacttttaccaa-ttatatgtcattctttagttctaagctgtactgcaagtcagtctggaactttatccacactaaaacttatcctatcgagtaattgtttttacacttttagACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
|| | | | |||| || || || | | ||| | | | | || | ||| || |||| ||| | ||| | ||| ||| || ||||| ||||||||||||| ||||| || ||||||||| ||||||| || ||||| |||||||| ||| ||| || | ||||| ||||| || |||| |
---------------------------------------aacgtggaatgacttatggaggatgaggtaattaca-----tcatgctattgaatttgta---ttagttgcaacaaaaattaac-tatttataaatgattt----ggttgtagACACCTGATGAGATAAAGGAGTATAGGGAGAAGAAACTGAACAGTCCTTGGAGAGACAGACCAATTTCAGAGTCATTGAAACTCTTTGAGGATATGAAAA
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 12
gttgaatcaatttaaaatttctgacatatggattcctgttacttttaccaattata-tgtcattctttagttctaagctgtactgcaagtcagtctggaactttatccacactaaaacttatcctatcgagtaattgtttttacacttttagACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
| | | | || ||| |||||| || ||| | || | | || | | ||| || ||| || ||| | | || || |||||| |||| || |||||||||||||| || ||||| |||||||| || |||||||| ||||| |||| |||||| | ||||||||||| |||||||||
----------------------------------------------gcatgtgaaagtgaaattttttagtcttagcatgtttacctcgtattcattggtattggttta-actgaagattactaatgggaataaatat-----catttctagACTCCTGAAGAAATAAAAGAGTACAGGGAAAAGAAGATGAACAGTCCTTGGAGGGATAGACCAATTGCAGAATCGTTGGAACTTTTTGATCAAATGAGAC
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 12
gttgaatcaatttaaaatttctgacatatggattcctgttacttttaccaattatatgtcattctttagttctaagctgtactgcaagtcagtctggaactttatccacactaaaacttatcctatcgagtaattgtttttacacttttagACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
| ||| | | || | | | || | | | || || || || ||| || | | | | | | | | || || |||| |||| ||||||||||| || || || ||||| ||||| || || |||||||| ||||| || |||||||| | ||||| ||||||||||||||||
---------------------------------------------aagaaatggtgatttcttttctgatgtta-gttcttttgttttgcattcatgaggtttttctatagttgagaaaagttatctaaaaagtcatt-----gattgcagACACCTGAAGAGATAAAAGAATATAGGGAAAAGAAGATGAATAGTCCTTGGAGGGATAGACCAATCGAAGAATCATTGAAACTGTTTGATGAAATGAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaactttatccacactaaaacttatcctatcgagtaattgtttttacacttttagACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
cactaaa putative branch site (score: 2)
tttttac putative PPT
agtaattgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaatcaatttaaaatttctgacatatggattcctgttacttttaccaattatatgtcattctttagttctaagctgtactgcaagtcagtctggaactttatccacactaaaacttatcctatcgagtaattgtttttacacttttagACTGCTGATGAGATAAAAGAGTACAGAGAGAAGAAAATGAACAGCCCCTGGAGGGACAGACCTATTGAAGAATCTCTAAAACTTTTTGATGAAATGAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA