Sequence
atgc intronic sequence ATGC exonic sequence...agcctctaatctcagagaggcctgtttgaatagttctctcttgaaattagacttttcaccaattgatgctaattgtgtagatttgttgttcttgttatagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 1
agcctctaatctcagagaggcctgtttgaatagttctctcttgaaattagacttttcaccaattg--atgctaattgtgtagatttgttgttcttgttatagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT
|| | | | | | || || | || | ||| ||| || | ||| | | ||| || ||||| | ||||||||| | ||| | || | | ||| ||| | |||||||| ||||||| |||||||| || || || ||||| |||||||||||||||||
ggcgattgaatttgccaaaattttgacgagaagcta-ctgtcactattgtctacttccttaaatactatgttgctgatgttgagggtatgttcg-atgtcagGTGATGCCCTATATAGTCTGCGCCAAAGTCTGAAAGATGCTAACAATGTGCTGCAGAGTTGGGATCCCACTCTGGTCAATCCATGCACATGGTTCCATGT
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G115420_T01 (Zea mays), 3'ss of exon 1
agcctctaatctcagagaggcctgtttgaatagttctctcttgaaattagacttttcaccaattgatgctaattgtgtagatttgttgttcttgtt-atagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT
| | || | || |||||| || | | || || || || | | | | | |||| | ||||||||| || | | || | | | ||| | ||||||||||||||||| |||||||| || || || ||||| || ||||||||||||||
-tattttgcatacaagctcatcaccgataaaagttcttatctgtttgttcatcttaactgggaatatacttgctgctgataatgttaccttttgtccacagGTGATGCCCTGTACAGCCTGCGTCAGAGCTTGAAAGATGCTAACAATGTCTTGCAGAGTTGGGATCCCACTCTTGTTAATCCATGTACATGGTTCCATGT
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
agcctctaatctcagagaggcctgtttgaatagttctctcttgaaattagacttttcaccaattgatgctaattgtgtagat----ttgttgttcttgtta-tagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT
| | || | | | ||| ||| | | ||||||| | | || | ||||| || ||| || ||| | |||| | ||||||||||||||||| | || | | ||| ||||| |||||||| ||||||| |||||||||||||||||||| || ||||||||||| |||||
tggcactgtttattgcaat-----tttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagacttttcaccaattgatgctaattgtgtagatttgttgttcttgttatagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT
tgctaat putative branch site (score: 2)
ttgttctt putative PPT
ttgttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcctctaatctcagagaggcctgtttgaatagttctctcttgaaattagacttttcaccaattgatgctaattgtgtagatttgttgttcttgttatagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - -aatctca
- - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - tctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgt