Sequence
atgc intronic sequence ATGC exonic sequencegtaatcttcttgcactcttacttctaatttatttatttctttttcttttgttagctaagttgttcttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G25060.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G34030.1 (Glycine max), 3'ss of exon 13
gtaatcttcttgcactcttacttctaatttatttatttctttttcttttgttagctaagttgttcttttggtgtgcgggatacctgacactg-ttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
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-----------gtactatttattgttgtattttaaattaggatgaatgcaatatctcaatg--tctcatgatttataactttccttgttttgattgaatattgtagCGTGTAGAGCCCGACAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 9
gtaatcttcttgcactcttacttctaatttatttatttctttttcttttgttagctaagttgttcttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
||| | | || | || || |||| | | | | | | | | || || | || || || || ||| || ||||| | || ||| || || ||||| ||| | ||||||||||| || ||||| ||| |||||||| | || ||||| ||||| ||||||||||| ||||
gta--cgttttattgttgtattttcaattaggatgaatgcaatctctcaatgtcatgatatactcacttt-tatg------acttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------------------------------------------gtaatcttcttgcactcttacttctaatttatt-tatttctttttcttttgtt-agctaagttgttc--ttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
|| || || | | | | || | || | ||| ||| | || || || |||| |||| | | | ||||||| | |||||||| ||| | || |||| |||| ||||| ||||||||||| || ||||| |||||||||||| | || |||||||||||||||||||| |||||||
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagctaagttgttcttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
acctgac putative branch site (score: 3)
ttaaatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcttcttgcactcttacttctaatttatttatttctttttcttttgttagctaagttgttcttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC