Sequence
atgc intronic sequence ATGC exonic sequencegtgagaggctcaagtctttatatcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 11
---------gtgagaggc--tca--agtctttat-atcttcaagttcagcttgtct-tgattaatttgcttatactgtgtcaatttctcccct-tttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
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agACAAAACTTAAAAATCCTTCAGTAATGTTTATTAATTTTTATTTGAGCTACTGAATTCTTAATCTTCTGTGATTG-ATCTATTGGTCTTGTGTTTGCAGACAAAACTTAAAAGTGCTGTTCAGCTGCAAGATCTGTTAGATGCCACAAGGATGCTGGTGCCTCGCACTAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 14
---------gtgagaggc--tca--agtctttat-atcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctcccct-tttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
| | || | ||| ||| ||||| | || | || |||| | | | | | | | || ||| || | ||||||||| |||||||| ||||| || ||| |||||||||| |||||||||||| | ||| | || || || || ||
agACAAAACTTAAAAGTCCTTCAGTAGTGTTTATTAATTTTTATTTGAGCTACTGAAATCTTAATCTTCTGTGATTGATCTATTGATCTTATGTTTGCAGACAAAACTTAAAAGTGCTGTTCAGCTGCAAGATCTGTTAGATGCCACACGGATGCTGGTGCCTCGCACTAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 11
----------------gtgagaggctcaagtctttatatcttca--agttcagcttg--tcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
||| | | | | | | | || | | || || | | || || | | || || | ||| ||||||||| |||||||| ||||| || || | |||||||| |||||||||||| | ||| ||||||| ||||| ||
gtgatattattttctagtgctaatgtaatatttgtcaacttttatttgatccactggattttttttttacctcttttgtttgatttaatgatcttttgtttgcagACAAAACTTAAAAGTGCTGTTCAACTTCAAGATCTGTTAGATGCCACACGCATGCTAGTTCCTCGTACCAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 13
----------------------gtgagaggctcaagtctttatatct--tcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
||| | | | || ||| | || | | || | || || | | || || | ||| ||||||||| |||||||| ||||| || || | |||||| | |||||||||||| ||||| ||||||| ||||| ||
gtgatattattttctagtgtttgtgtaatatttgtctacttttatttgatcttctggattttttttttttttacctcttttgcttgatttaatgatcttttgtttgcagACAAAACTTAAAAGTGCTGTTCAACTTCAAGATTTGTTAGATGCCACACGAATGCTAGTTCCTCGTACCAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 13
----------------------gtgagaggctcaagtctttatatcttcaa-gttcagcttgtcttgattaatttgcttatactgtgtcaatttct--ccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
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gtgcttactttcccttcatctttttctcattttgttttattgtattgtcaatattcttatttatgtaatcgcttattagatggtgcatttgttgatgatctcttttgcagACAAAACTCAAGAGTGCTATCCAGTTGCAAGATTTGTTGGATGCCACACGGATGCTTGTACCACGCACAAGMapped 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|124793068|gb|EH882747.1|EH882747EST: ACTATTAAACCTAATGTTGAAGTTACAATGGTGGAAAGCCAAGAGCTGAG ACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATG
genomic: ACTATTAAACCTAATGTTGAAG-TACAATGGTGGAAAGCCAAGAGCTGAGgtgagaggct ... ccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATG
EST:
gi|19874907|gb|AU235738.1|AU235738EST: AACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG ACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGA
genomic: AACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAGgtgagaggct ... ccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
gattaat putative branch site (score: 3)
tcaatttctccccttt putative PPT
attaatttgcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaggctcaagtctttatatcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA