Sequence
atgc intronic sequence ATGC exonic sequencegtatgagttctgtacattgtttatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtctttcataatctttctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65430.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
gtatgagttctgtacattgtttatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtc-tttcataatctttctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
||| |||||| | | ||| ||| | | || || ||| | |||||| ||| || ||| || ||| | | || ||||||||||| |||||| | |||| |||||||||||||| |||||||||||||| ||||| ||||| | |||||| ||||||| |||
gtac-agttcta-atctgagatattttcttaa-tact--ttattatttttatttaatattgtggttaatttgtgctgcttcgcactggtt----acagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
gtatgagttctgtacattgtttatgttcctgactaac-aactaatatgtctatttatctttgaacatattttttgtctttcataatctttc--tgtg----cagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
||| | ||||| | | | || | | | | | | | || | | | ||||| || ||| | || ||| |||| ||||||||||| |||||| | |||| |||||||||||||| |||||||||||||| || || ||||| |||||||| ||||||| |||
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatt-tgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
gtatgagttctgtac-----attgtttatgttc---ctgactaacaactaatatgtc-tat-ttatctttgaacatattttttgtctttcataatctt-tctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
||| ||||||| | || ||| || ||||| ||| | ||| | | || | | || || ||| | ||| | || | | ||||||||||| |||||| | |||| |||||||||||||| ||||||||||| || || || ||||| |||||||| ||||||| |||
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 9
gtatgagttctgtacattgtt-tatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtct---ttcataatctttctgt-gcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
| | ||| | |||| | || ||| | ||| | | ||| || || | | || |||| | | | | | |||||| |||||| || |||||||| | | | || | || || ||||||||||||||||||| || ||||||||| | |||||| ||||||| |
gcagctcatctttgggatgttgtgattttctgtgtggatgcta-tgt-tcttttcatttccaaggatgttttctcctcaaacttaaattgcttctgttgcagTACGACGAGACTGATGCAAGGAGGGAAAGAGCTAAAAACTCTCTTGAGAGATATATGCATTACTATGAGCGCTGGGCATCCAATCAGACA
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 9
gtatgagttctgtacattgtttatgttcctgacta-acaactaatatgtctatt-tatctttga-acatattttttgtctttcata-atctttctg--tgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
|| | | | | | |||| | || | | ||| | | | | | | | ||| || || || || ||| |||||||||||||| |||| ||||| | || ||||| ||||||||| | ||||||||||| || || ||||| ||||||| ||||| |||||
---tggtcctcgcccccttagaaatgtattgacggtgctacagaagtatcttctatggcactaatgggaaggtgctgtacttgatttattttgctgcttgcagTATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgtctatttatctttgaacatattttttgtctttcataatctttctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
aactaat putative branch site (score: 2)
tctttctgt putative PPT
tatttatctttgaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagttctgtacattgtttatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtctttcataatctttctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG