Sequence
atgc intronic sequence ATGC exonic sequencegtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 11
-------------------------------------------------------------------------------gtgattg--gcaaaatcaagaattttgaaat--tttttgcaaattgcttgctcttactgcat------tttcaactatttccca---tctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
||| || | | | | || ||||| | | |||| ||| ||| || | || | |||| | | | ||||||||||| |||||||| | ||||| ||||| ||||| || |||||||| |||||||||||||||||||||||||| ||||| | |||||||
gtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttagGTTGGAGCTGAAATTGTAAGGAGAGCGCTGAGCTACCCGCTTAAATTGATTGCTAAGAATGCTGGTGTTAATGGAAGCGTTGTTACCGAGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 11
--------------------gtgattggcaa--aatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaa--ctatttcccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
| |||| | | | | | || | | ||| || || || || || | ||| || ||||||| || ||||| || | | | |||||||||| || ||||| ||||| || |||||||||||||| || |||||||| | ||||||
gtaggaaaacaaatgaaataatctttggttattgtttcatttcatcctaggttcaaggcatttgttttctattgtcaataattaaaatttctttttggcttcaagGTTGGGGCTGAAATCGTAAGGAAGTCCTTGAGTTACCCACTTAAATTAATAGCAAAAAATGCTGGTGTTAACGGCAGTGTTGTTACTGAGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------gtgattggcaaaa-tcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctct--agGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG-------
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gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------gtgattggcaa-aatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctct--agGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
||| | || || || || | ||| | | ||| | | | || || || | | | || | | |||||||||| || ||||| |||||||| || ||||||||| ||||||| || || |||||||||||||| ||||| ||||||||||| ||||||
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.3 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------gtgattggcaa-aatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctct--agGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
||| | || || || || | ||| | | ||| | | | || || || | | | || | | |||||||||| || ||||| |||||||| || ||||||||| ||||||| || || |||||||||||||| ||||| ||||||||||| ||||||
gtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcaggttggagCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------------------gtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccat--ctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
||| | || || | | | || ||| | | | || || || | | | || | |||||||||| || ||||| |||||||| || ||||||||| ||||||| || || || || |||||||| ||||| ||||||||||| ||||||
gtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAAAACGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------------------------------gtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttc--ccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
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gtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATTGCCAAAAATGCTGGTGTTAATGGAAGTGTGGTCAGTGAGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------gtgattgg--caaaatcaagaattttga--aattttttgcaaattgcttgctcttactgcattttcaactattt-----cccatctct--agGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
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gtaagtgatattttatgctattcctacaatcaagttacaatcaaggtttgacatgaagccgatacaacttaacttgttatgttcagatctgaattgtctgggtgcctacttctgcagGTTGGCGCTGAGATTGTGAGGCGGGCCTTGTGTTACCCTTTGAAATTGATCGCCAAGAATGCTGGTGTGAACGGAAGCGTGGTGGTTGAGAAGMapped 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|125261013|gb|EL275098.1|EL275098EST: ACCCTTGAAAATGATGAAGAAAAG GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATA
genomic: ACCCTTGAAAATGATGAAGAAAAGgtgattggca ... ccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
ctcttac putative branch site (score: 3)
ctatttcccatctct putative PPT
attttcaactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG