Sequence
atgc intronic sequence ATGC exonic sequencegttagatattcaacgtacttgtcatattagtacttataaaagtaacagagattgaaactagaagctctttctgcttgaatagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53620.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------gttagatattca-acgtacttgt-catattagtacttataaaagtaacagagattga-aactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
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gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
----gttagatattcaacgtacttgtcatatt-----agtacttataaaagtaacagagattgaaactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
||| | | || | || || | | | | | | | |||||| || || || ||| || |||| |||||||| || ||||| ||||||||||| ||||| ||||| |||||||| |||||||| || |||| |||||||| || |||||| | ||||| |
gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaa--taaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
----gttagatatt-----------caacgta-----cttgtcatattagtacttataaaagtaacagagattga-aactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
|||||||||| ||| | | || | || | | || ||| |||| | | | || || | ||| ||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||| | |||||||| || |||| || ||||| ||||| ||| | ||||| |
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
----gttagatattcaacgtacttgtcatattagtacttat---aaaagtaacagagattgaaactagaagctctttctgct--tgaatagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
||| | || | | | | || ||| | | || | | |||| || || || |||| || | |||| |||||||| || || || ||||||||||| ||||| ||||| |||||| | |||||||| || |||| |||||||| || |||||| | ||||| |
gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaatactgaa--taaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------gttagatattcaacgtacttgtcatattagtacttataaaagtaacagagattgaaactagaagctctttctgcttgaa----tagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
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gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgt--aaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAAMapped 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|125278488|gb|EL292573.1|EL292573EST: CCAAAGCTATTGGTCTGATGCCAATGATTGATCAG GGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTAT
genomic: CCAAAGCTATTGGTCTGATGCCAATGATTGATCAGgttagatatt ... gcttgaatagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtacttataaaagtaacagagattgaaactagaagctctttctgcttgaatagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
aagtaac putative branch site (score: 2)
ctctttctgctt putative PPT
ttataaaagtaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagatattcaacgtacttgtcatattagtacttataaaagtaacagagattgaaactagaagctctttctgcttgaatagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT