Sequence
atgc intronic sequence ATGC exonic sequence...tgccgaattctttttttcaatttctaacttttgtttgttctgcgcaaagattgatagtatgaattgaacgataaaatcggtggacattgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77440.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77440.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 1
tgccgaattctttttttcaatttctaacttttgtttgttctgcgcaaagattgatagtatgaattg-aacgataaaatcgg---tggacattgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG
|| | | | | | | | | |||| | || ||| | |||| || ||| | ||| | | ||||||||||||||||| || || ||||| || || ||||| |||||||| |||||||| || || || || ||| | || || ||||| | || || | |
--gtgagtgccccccgcgatccccctcccccttctccgctcccacaaaaccctagcgtctgatccgcggcgatggcgggggatttggggttcgtgtcgctgcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGGCGCCTCGGGGTGCAGCTGCAGACGGTCG
upper sequence: AT1G77440.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 1
----------tgccgaattctttttttcaatttctaacttttgtttgttctgcgcaaagat--tgatagtatgaattgaacgata------aaatcggtggaca------ttgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG
| | || || ||| ||| || | | | | | ||| | |||| | | | || | | | | ||| | | | || | | |||||||||||||||||| || || ||||| || || ||||| |||||||| |||||||| || || || || || | || || ||||| | || || || |
gtgagtgccctccggagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagattgatagtatgaattgaacgataaaatcggtggacattgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG
gattgat putative branch site (score: 4)
ataaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgccgaattctttttttcaatttctaacttttgtttgttctgcgcaaagattgatagtatgaattgaacgataaaatcggtggacattgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG
- - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - caaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaat