Sequence
atgc intronic sequence ATGC exonic sequenceTGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtattcgtacattcccaagttgcagagagtatacctgagaacaacaacggataatttttttgggtttttgatttcttaaaactaagttttttttatttattgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05090.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA19G42990.1 (Glycine max), 5'ss of exon 6
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtat----tcgtacat-tcccaagttgcagagagt---atacctgagaacaacaacggataatttttttgggtttttgatttcttaaaa---ctaagttttttttatttattgcag--------------------------------
|| |||| |||| ||| ||||||||||| || ||||| ||||| ||||| |||||||| | ||||| || || || |||||||| |||||||||||| | | | || | | || ||| | ||| | ||| ||| || | ||| | | | | | ||| ||| | | | || | | | |
GGGATACATTCCAATTGCTGCCAAAGGCCATAAAGATTCTGTTTATGCATTGGCTATGAATGAAAGTGGAACAATTCTTGTCTCTGGTGGCACAGAAAAGgtacaatatggcatatgctctgaattattgaggcttctttacatttgaa--acagtagagagggtttcttgcgctgtagtagcttgaaagttttgggatgttgtctctgaccatggcttatttcttcaacttttttggggttcactag
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G30050.1 (Glycine max), 5'ss of exon 5
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgta--ttcgtacattcccaagttgcagagagtatacctgagaacaacaacggataatttttttgggtttttgatttcttaaaactaagttttttttatt-tattgcag-----------------------------------------------------------------------------
|| |||| |||| ||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||| | || || || ||||| |||||||||||| | ||||| | || || | | | | | || | || ||| | | | || | | ||| |||| |||| |
AGGATACAATCCAATTATTGCCAAAGGCCATAAGGAATCTGTTTATGCATTGGCAATGAATGAAGGTGGAACACTTCTTGTCTCCGGTGGTACAGAAAAGgtaaaatgtggcattcttgttcagatttatgttctcccgtgtgtggcttctgctagctatt----acccttggaatataagaagcatttactttatattatattaaattgaatttcattagctagatagtggggtgttatctctacctagagcattatttatttttatttattttttcttttaag
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA19G43070.1 (Glycine max), 5'ss of exon 6
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtattcgtacattcccaagttgcagagagtatacctgagaacaacaac------ggataatttttttgggtttttgatttcttaaaactaagttttttttatttattgcag
|| ||| |||| ||| ||||||||||| || ||||| ||||| ||| | |||||||| | ||||| || || || |||||||| |||||||||||| | | ||| || ||| | | || || | |||| | ||| |||||| || | |||| | | | ||
GGGATACGTTCCAATTTCTGCCAAAGGCCATAAAGATTCTGTTTATGCATTGACTATGAATGAAAGTGGAACAATTCTTGTCTCTGGTGGCACAGAAAAGgtaca-atgggctagtttgttt--aagcttattttttaaaataattgcttttcaaaataaaataagcacttttatgattttctag---tgtgtttgtctaaattga-----
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA03G40440.4 (Glycine max), 5'ss of exon 6
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtat--tcgtacattc---ccaagttgcagagagt---atacctgagaacaacaacggataatttttttgggtttttgatttcttaaaacta--agttttttttatttattgcag--------------------------------
|| |||| |||| ||| ||||||||||| || ||||| ||||| |||| |||||||| | ||||| || || || |||||||| |||||||||||| | |||| | | ||| ||| | ||||| ||| | | || ||| |||| | ||| | | || || | | || | ||| |
GGGATACATTCCAATTGCTGCCAAAGGCCATAAAGATTCTGTTTATGCACTGGCTATGAATGAAAGTGGAACAATTCTTGTCTCTGGTGGCACAGAAAAGgtacaatatggcatttgctctgacttgtcgaggcttctttacctttgaaacattagatatggtttgtttgcgctttagtagcttgaattttatgggatgttgtctcttaccatggtttatttcttcaatttatttggggttcactag
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA03G40360.1 (Glycine max), 5'ss of exon 6
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtat--tcgtacattcccaagttgcagagagtatacctgagaac----aacaacgga--taatttttttgggtt-tttgatttcttaaaactaagttttttttatttattgcag------------------------------------------
|| |||| |||| ||| ||||||||||| || ||||| ||||| ||||| |||||||| | ||||| || || || || ||||| |||||||||||| | ||| | | || | || | |||| ||| || | | ||| || ||| | | | || |||||| | |||
GGGATACATTCCAATTGCTGCCAAAGGCCATAAAGATTCTGTTTATGCATTGGCTATGAATGAAAGTGGAACAATTCTTGTCTCCGGTGGCACAGAAAAGgtacaatatggcatatgaatgaaagtgaaacaattcttgaggcttctttacatttgaagcagtagagatggtttgcttgcactgtagtagcttgaattttttgggatgttgtctctgaccatggtttacttcttcattttttttggggttcactag
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 5'ss of exon 6
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtattcgt--acattcccaagttgcagagagtatacctgagaacaacaacggataatttttttgggtttttgatttcttaaaactaagttttttttatttattgcag
||| || || ||| |||||||| || |||||||||||||| ||||| |||||||||| ||||| | || |||||||||||||| || ||||||| | | ||| | || | || | | | || | | ||||| || | | ||||||||| || ||||||||
TGGATATGTGCCTGTTGCTGCCAAAGGCCACAAAGAGTCTGTGTATGCATTGGCAATGAATGATAGTGGAACCCTTCTTGTTTCTGGTGGAACTGAGAAGgtatgctatgatatttatagtttctttattgtcttcatttttg-aaggatcgttaattcttccttgcatctgatttcttttttatataagaaatttattta------Mapped 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|124710930|gb|EH802332.1|EH802332EST: GGCGATGAATGATACCGGAACGATGCTACGTTTCTGGTGGAACAGAAAAG GTTTTACGTGTCTGGGACCCTAGAACCGGTT
genomic: GGCGATGAATGATACCGGAACGATGCT-CGTTTCTGGTGGAACAGAAAAGgtattcgtac ... tttattgcagGTTTTACGTGTCTGGGACCCTAGAACCGGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGGTACACACCAACAATTGCGAAAGGCCATAAGGAGTCTGTGTATGCTTTGGCGATGAATGATACCGGAACGATGCTCGTTTCTGGTGGAACAGAAAAGgtattcgtacattcccaagttgcagagagtatacctgagaacaacaacggataatttttttgggtttttgatttcttaaaactaagttttttttatttattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA