Sequence
atgc intronic sequence ATGC exonic sequence...tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G23070.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 3
--------tgtttaccttac-ttgacttttgaatcca-ctagccttcagttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgc-agGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
|||| | ||| || |||| |||||| | | | | | || || || ||| || || | ||| ||| |||| ||| |||| |||||| |||||||||| ||||||||||| | |||||||||||||||||||| ||||||||||| |||||||| || ||||| | || || |
ggatctatagtttgcattaaattattttttcaatccaaccatttcgtattgcttgtggctatcaacttg-----gaagcgctaagttattt------ggaatttctgccagGCACTGGATTATTGCCATTCACAAGGAATCATGCATCGTGATGTGAAACCACATAATGTAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 3
--------tgtttaccttacttgacttt-tgaatccactagccttcagtta-taaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
||| | || | | ||| | |||||| | | || | || || || ||| || || | ||| || | || ||||| |||||| |||||||||| ||||||||||| | |||||||||||||||||||| ||||||||||| |||||||| || ||||| | || || |
tgatctataatttgcaatagattattttatcaatccaaccatttcctattgcttgtggctatcaacttg-----gaagcgctaagttaattg-----gaagttctgccagGCACTGGATTATTGCCATTCACAAGGAATCATGCATCGTGATGTGAAACCACATAATGTAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 3
----tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaac-atttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
| || | | || ||| | | || || | | | ||| || | | | || || | ||||||| || ||||||||| || |||| |||||| |||| || |||||||| ||||||| || ||||||||||||||||||||||| |||||||| ||||||||| | || || |
cattggcatattgcatatattttacgaagt-attcatgttggtttgttagg----tgaactttcatttagttaacttggtagaatctttttctttatatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCACATAATGTCATGATTGATCATGAGCAGCGTAAACTTCGTCTTATAGATT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 4
tgtttaccttact-tgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgt--ttgttgtttctttttaac---atttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
|| || | | || | | | | || || ||| | | | || || | | || || | | || ||||||| ||||| | ||||||||| | || ||||||||||| |||||||| ||||| ||||| |||||||| |||||||| ||||| || | | ||||| |
------ccccaccaccgccaataaaaaaaacgaatagaaaggaaatgaagttcggttttctactttacccttcaattttggattattgatggctttatcactgcagGCTTTGGACTACTGCCATTCTCAAGGGATCATGCACAGGGATGTGAAGCCACACAATGTAATGATTGACCACGAGCAACGAAAGCTGAGACTGATTGATT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgtt--gtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
|| | || | | || | | | | || | ||| | | ||| || | | | | | | | || | | | | ||||| ||||| | ||| ||||| | || || |||||| |||| || |||||||||||||| ||||||||||| || ||||||||| | | ||||| || |
-attatgataacaacaacaataaaactaattgtaa-caatcatagtatgaggtattttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------tgtttaccttacttgacttttgaatccactagccttcag---ttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
||| || || | | | | | ||| | | ||| | | ||| || ||||| ||| || || | | | ||||| ||||||| ||| ||||| | || || ||||| |||| || |||||||||||||| ||||||||||| |||||||||||| | | | || || |
gtaggttctacctaaactttgctcggcttgcattcaatcattacacttaattttcagtgttctatttatctgaattttagttgtgtatctgcttaaagaaacgtgcttgatgcgccgcagggctaagaaaaattgtggcattggctc-aatgcttgatgtagtcgtggctttgccctgtttcagGCCTTGGATTACTGTCATTCGCAAGGGATAATGCATCGAGACGTCAAACCACATAATGTGATGATTGATCATGAGCAGCGAAAATTAAGGCTCATCGATT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 3
tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
|| || || | | | ||| | | | | |||| |||| ||| ||| ||||||| | ||| |||||| || | ||||| |||||||| || ||||| || || ||||| |||||||||||||||||||| || || || | || ||||
---------------------------gtgaggttt---tttaaccccatgtggattggacttgggaggattttgatgttgctt------gtttttgcagGCACTCGATCACTGCCACTCGCAAGGAATTATGCACAGGGACGTGAAGCCGCACAATGTGATGATTGATCACGAGCAGCGCAAGCTGCGCCTCATCGACT
upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 3
tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
|| || || | | | ||| | | | | |||| | || ||| ||| ||||||| | ||| |||||| || | ||||| |||||||| || ||||| || || ||||| |||||||||||||||||||| || || || | || ||||
---------------------------gtgaggttt---tttaaccccatgtggattggacttgggaggattttgatcttgctt------gtttttgcagGCACTCGATCACTGCCACTCGCAAGGAATTATGCACAGGGACGTGAAGCCGCACAATGTGATGATTGATCACGAGCAGCGCAAGCTGCGGCTCATCGACTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47831931|gb|CK121615.1|CK121615EST: CAACTCTCTCAGACTATGATGTTCGATATTACATTTTTGAACTTCTAAAG GCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCA
genomic: CAACTCTCTCAGACTATGATGTTCGATATTACATTTTTGAACTTCTAAAGgtaattattc ... atttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCA
EST:
gi|124715188|gb|EH806590.1|EH806590EST: CAACTCTCTCAGACTATGATGTTCGATATTACATTTTTGAACTTCTAAAG GCGTTGGATTTCTGCCATTCACGTGGAA
genomic: CAACTCTCTCAGACTATGATGTTCGATATTACATTTTTGAACTTCTAAAGgtaattattc ... atttatgcagGCGTTGGATTTCTGCCATTCACGTGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
ttttaac putative branch site (score: 2)
ttgtttctttttaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgttgtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - aatccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc