Sequence
atgc intronic sequence ATGC exonic sequence...acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28760.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
--acattcattacccgtgg-tgatgcaacaactatactaacacaaatca-ctatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
| | || || ||| || || || || | | | | | ||| || | | |||| || || | |||| ||| ||| || ||||| |||||| | || ||||||||||||||||||||||| || || ||||||| ||||||| |||| ||||| |||||
ttataaacagggattttgtctgaaagaatcccttagtctgcataacttaatttttcttgatgccttgtttaaccaacatttctttcat--tcttgaccata--gTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG-------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
acattcattacccgtggtgatg-caacaactatactaacacaaatcactatgatccatgt-agtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
||| | | | || |||| | | || | || | | | ||| | | | | || | |||| | | | | |||||| |||||||| || |||| || |||||||||||||| ||||| || || || ||||| ||||||||| |||| ||||| |||||
acaatgct--cttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG-------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 3
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattg--atttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
||| | || | || | | ||||||| | || || | || | | | | | || | | || | ||| | | | |||||| || ||||| |||||||| || |||||||||||||||||||| || || | ||||| | ||||||| |||| ||||| |||||
caattgaatattgcttttgcagaagcaactattttg-cataagcctctttttcttgtattgatgccttgtttaccagtatttctttcattcttgata-acagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG-------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
-------acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
| || | | || | | ||||| || | | || ||| || | | |||| || || | |||| ||| ||| || ||||| || ||| | || ||||||||||||||||||||||| || || || |||| ||||||| |||| ||||| |||||
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctgg---atgccttgtttaaccaacatttctttcat--tcttgaccata--gTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG-------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaa-attgatt--tgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
| | | | || | | ||||||| | || | | || | || ||| || | || | | || | ||| | | | | |||| || ||||| |||||||| || |||||||||||||||||||| || || | ||||| | ||||||| |||| ||||| |||||
tttgtgaatgtggcttttgcagaagcaactattttg-catgagcctcttttttct-tgtcttgatgccttgtttaccagtattctttcattcttgata-atagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG-------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 2
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
|| | | | | || | || | | || || | | | | | | || |||| | | | | | |||| |||||||| || |||| || |||||||||||||| ||||| || || || ||||| ||||||||| |||| ||||| |||||
caatgctcttgtcaggatgtcttactttacatgatcatttttttccctttccttacgtgaattcttggttttacaatgttcctttcatctctgacaaaagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG-------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
-acattcattac--ccgtggtgatgcaacaactatactaacacaa-atcactatgatccatg--tagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
|| |||| || | || | || || | |||| || | ||| ||| | || | | | | ||| || | | |||| ||||| |||||||| || ||||| || ||||||||||||||||||||||||||| | || || || ||||| |||| |||||||||||
tccaatcatcacattcatgccaacacatca-ttgcactagatcattacttttattatctttaactaattcct-acagtaattcctttcac--tcttgatg--gcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
aattgat putative branch site (score: 4)
aatgattttgaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA