Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagcccttattttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G05940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g42200.1 (Oryza sativa), 3'ss of exon 3
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagcccttattttccaat----ttataattcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
| || || || || ||| ||| ||||| | ||| | | | |||| | | | | || | | | | |||||||||| |||||| || || ||||||||| | ||||| ||||| || || || |||||||| || ||||| || || ||||||||||| || |||||||
------------------------------------------------------------------------------------------cccactttaaagcccattcattagtaataagcccaagtaagagaatcgcatcaaatgggctaatggtttttgggc-ctgtgaattttgtccctccctccagGATTACAAGGCGAAGCTGTCGGACTTCGGGCTGGCCAAGGACGGGCCGGAGGGGGACGACACCCACGTGTCGACGCGCGTGATGGGCACCCATGGCTACG
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g53750.1 (Oryza sativa), 3'ss of exon 3
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagccctta--ttttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgtttt-cagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
| | | | || | | | || || |||| | | | |||| || | ||| | |||| | | | | ||||||||||||||||| ||||| ||||||||| | ||||| || || || | || |||| || || || | || || || ||||| || || || ||||
----------------------------------------------------------------------------------------taaagttagtagttggctatactattaaacttgctcttagctatagttaattatgatgttgtggctgacggagagatt--tatattatgttgggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAGGGGGACGCGACACACGTCACGACCCGCGTCATGGGGACCCACGGGTACG
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G19600.1 (Glycine max), 3'ss of exon 3
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagcccttattttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
| || | | |||| | || | | || | ||| || | | | ||| ||| | | || || | |||| || ||||||||||||| || || || ||||| || ||||| || |||||||| || |||||||| || ||||| || ||||| ||||| ||||| ||||| |||||||
------------------------------------------------------------------------------gttcaaatatc-attcttatttttaatattcttcaatgattt-ctcttcttggatataatgttgttcttaatactt-----actcttct-cattaaatatt-ctttcagGATTACAATGCAAAGCTATCTGATTTTGGGTTGGCAAAAGACGGTCCCGAAGGAGATGATACTCACGTTTCAACCCGAGTTATGGGTACACACGGCTACG
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G05660.1 (Glycine max), 3'ss of exon 3
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaa--aagcgtttacaaccgaaattaacagtcgt-taccaatcagcccttattttccaatttataattcctaaagttctaaa----gaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
| || || | |||| | | || | | | | | ||| | | ||| | | | | |||| || | | || || || | ||| | || |||||||| | || ||||| || || || || || |||||||| || || |||||||| ||||| || || |||||| |||| ||||||||||||||||| |
------------------------------------------------------------------------------gtaagtaatcaattactagtcactttctctgacatactctaattaatgcaccgtttggacaatttcactccttaattaatcaattattaactcactctttttaattattcttccagGATTATAATGCAAAACTTTCCGATTTTGGCTTGGCCAAAGATGGTCCTGAAGGAGATGACACACACGTTTCAACTAGAGTCATGGGCACACAAGGCTATG
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G08110.1 (Glycine max), 3'ss of exon 3
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagcccttattttccaatttata--attcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
|| || || | | | | || | | || || ||||| | | | || ||| ||| || | || || | ||| || ||||||||||||| || || | ||||| || ||||| || |||||||| || |||||||| ||||| || || ||||| ||||| ||||| ||||| |||||||
---------------------------------------------------------------------------------gaaatagatataagatattcttatattcttcaaggatt-gctcttatatgggatataatgttgttcttaatactc-----actcttct-catttaatatt-ctttcagGATTACAATGCAAAGTTATCTGATTTTGGGTTGGCAAAAGACGGTCCCGAAGGAGATGACACCCACGTTTCAACCCGAGTTATGGGTACACACGGCTACG
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G17050.1 (Glycine max), 3'ss of exon 3
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgt-taccaatcagcccttattttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
| | || | |||| | | || | | | | | ||| | || ||| | | | ||||| || | || || | | || | || |||||||| | || || || ||||| || || || || ||||| || || |||||||| ||||| || || |||||| |||| ||||||||||||||||| |
----------------------------------------------------------------------------gtgaataatcaattactagtcactttctctggcatactctaattaatgctccgtttgaacaatttcattccgtaatcaatttttaactcactctcttcattcattcttccagGATTATAATGCAAAGCTTTCTGATTTTGGCTTGGCAAAAGATGGTCCCGAAGGAGATGACACACACGTTTCAACTAGAGTCATGGGCACACAAGGCTATG
upper sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S207_2V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagcccttattttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgttt-tcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
|| | || | | || |||| || ||| || | ||||| | ||| ||| || | |||| | | | || | || || |||||||||||| || || || ||||| |||||| |||| ||||| ||||| ||||||||| | ||||| || ||||| || || |||||||| | ||||| |
-------------------------------------------------------------------------------cagtaacgagt-tgcgtggaagtaac-gttattataaagcg----ttattgttgcatt-atacctctt--agtttgtcctctgtcctcagacttgtttatggttgtcagGATTACACAGCCAAGCTGTCTGATTTCGGGCTAGCGAAAGATGGACCTGAAGGAGACAAAACTCACGTTTCAACACGTGTTATGGGCACCTATGGCTATGMapped 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|124774542|gb|EH864671.1|EH864671EST: ATCCTGTTATCTATCGGGATTTCAAAGCCTCCAATATCTTGTTAGATTCC GATTACACGGCGAAACTCTCTGACTTCGGG
genomic: ATCCTGTTATCTATCGGGATTTCAAAGCCTCCAATATCTTGTTAGATTCCgtaagtaaca ... ttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatttataattcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
ttctaaa putative branch site (score: 2)
tcttgttttc putative PPT
tataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagcccttattttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgttttcagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA