Sequence
atgc intronic sequence ATGC exonic sequencegtaaatatcgaattctagatttatttttttgtttgattcttttgaaaaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02610.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01630.1 (Glycine max), 3'ss of exon 1
----gtaaatatcgaattctagatttatttttttgtttgatt--cttttgaaaaccg-atattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
||||| ||| | | |||| ||||| || |||| || || | | |||| | || |||| || || |||| ||||||||||||||||| || |||||| |||||||||||||| |||| ||||||||| |||||||||
gtaaataaatccacaatctcttaacaacttttatgtttactttactttagagaatcttgtcatgatcatcttagttttattc--ttcagTTTGCTCACAGAGATTGCATTCAGACATGGTGCGATGAGAAAGGAAATACAACTTGTGAAATATGTCTCCAG
upper sequence: AT1G02610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G01680.1 (Glycine max), 3'ss of exon 1
gtaaatatcgaattctagatttatttttttgtttgattcttttgaaaaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
|||||| | | | | |||| ||||| || ||| | || ||| || |||| ||| || |||| ||||||||||||||||| || ||||| ||||||||||||| |||| ||||||||| |||||||||
gtaaatccacattctcttaacaacttttatgtttactttgtttttca-tgaatcttgtcatgattagttttattg--ttcagTTTGCTCACAGAGATTGCATTCAGACTTGGTGCAATGAGAAAGGAAATACAACTTGTGAAATATGTCTCCAG
upper sequence: AT1G02610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G37740.1 (Glycine max), 3'ss of exon 1
----------------------------------------gtaaatatcgaattctagatttatttttttgtttg--attcttttgaa----aaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
| | | || | | |||||||| | || ||| |||| | || | || | | ||| ||| | |||| ||||| |||||||||||||| ||||||| | || |||||||| |||| |||||||| |||||||||
gtaagtaatcacataatacataatttcttaatcttaagcacttgtttttctgttattaacttatttttcttcctggaattttttttcattttaattctcgtcaataactgcgtttttgttt--tgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG
upper sequence: AT1G02610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G40340.2 (Glycine max), 3'ss of exon 1
-----------------------------------------------gtaaatatcgaattctagatttatttttttgttt----gattcttttgaaaaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
| ||| || | | |||| || || || |||| |||| || | || || | | ||| |||| |||| ||||| |||||||||||||| ||||||| | || |||||||| |||| |||||||| |||||||||
gtaagtaaacacagaatacataagacgcaatttcttaatcttaagcacttgttattttgttattaagctattattatgcttccttgatttttttttaattct-catcaataactgcgtttttgttgcgc--agTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtttgattcttttgaaaaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
tattgat putative branch site (score: 3)
tttcgtt putative PPT
atattgattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatatcgaattctagatttatttttttgtttgattcttttgaaaaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA