Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G21930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
| | | || | | || |||| ||| | ||| | ||| | |||| ||| ||| ||| |||| ||| || | ||| |||||||||||||| || || |||||||| ||||| || ||| | |||||||| || | |||| | || |||| |||||||||||| || |
ctaattacttcctaccgcattact------tgaactgatttggtgattgatgaattaaca-gttgaatatgttttgcataataat------gttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
upper sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
| ||| | || |||| ||| | ||| | ||| | |||| ||| ||| ||| |||| ||| || | ||| |||||||||||||| || || |||||||| ||||| || ||| | |||||||| || | |||| | || |||| |||||||||||| || |
------cttcctaccgcattact-------tgaactgatttggtgattgatgaattaaca-gttgaatatgttttgcataataat------gttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
upper sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
| | || || | ||| ||| || | | || | | | | ||| | ||| | || || | || ||||| |||||||||||||| ||||| |||||||| || || |||||| ||||||||| |||| | |||| ||||||| ||||||||||||||| |
-------------ttgtcttcgtaaaag-----atgctatttcttgtcttattgacaattcttacattcttgtt--gagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
|| ||| | || || | || ||||| |||||||||||||| ||||| |||||||| || || |||||| ||||||||| |||| | |||| ||||||| ||||||||||||||| |
-----------------------------------------------------------------------------gta-taagctcctcatgtgagtattgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
| | |||| | | ||||| | ||| | | || | | || | || ||| | || || | || ||||| |||||||||||||| ||||| || ||||| || || |||||| |||| |||| |||| | |||| ||||||| ||||||||||||||| |
----------------acctcttgcctttgtaaaagatgctatttattgtcttaacttcttaca---ttcttgttgagta-taagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
| | | || | | || | || || |||| | | | || ||||||| | | | || |||| |||||||||||||||||||| ||||| |||||||||||||| |||||| | ||||| | || | | | ||||||| |||||||||| |||| ||
-------------------cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagca-ggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
tttcaatagtaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG