Sequence
atgc intronic sequence ATGC exonic sequence...ttaattttgcttttgtagtcatggtttctgcattgttcagagatttcaatttttggctctcttggaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G45190.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G45190.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 2
-----ttaattttgc--ttttgta----gtcatggtttctgcattgttcagagatttcaatttttggctctcttggaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG
||| ||| | | ||||| || | ||| | |||| | ||| || || | | | || | | || | | | ||| || ||||| || ||||| || || |||||||| |||||||| ||||| |||| ||||| ||||||||||||||| |||||
gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattg--taatgttggcccctg--cagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
upper sequence: AT5G45190.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 1
---ttaattttgc--ttttgtagtcatggtttctgcattgttcagagatttcaatttttg--gctctcttggaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG
||| ||| | | |||| | || | | || ||| || || || | || | | | || || | || ||| || ||||| || ||||| || || |||||||| |||||||| ||||| |||| ||||| ||||||||||||||| |||||
tgcttattttcaccatgttgtgaattttgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattgtaatgttggcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
upper sequence: AT5G45190.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 1
---ttaattttgcttttgtagtcatggtt-tctgcattgttcagagatttcaatttttggctctcttg----gaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG
| | ||| |||| | || || | | | || || ||| || | | | ||| | || | |||| ||| |||||||| || ||||| ||||| ||||| || |||||||| ||||| || ||||||| || ||||||||||||||||||
ccataacatttttttttatcagaataattatataacatttttttttatcagaataattatataccataacatgaatattagaaatctggtttcattg-cagACCCCAGGTAACTATAGCCACAGCAATAATATTTTGTCATCGGTTCTTTCTTTGCCAATCTCACGCAAAGAATGACAGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatttttggctctcttggaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG
cgctgat putative branch site (score: 4)
tcccc putative PPT
atatagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattttgcttttgtagtcatggtttctgcattgttcagagatttcaatttttggctctcttggaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - gcttttg