Sequence
atgc intronic sequence ATGC exonic sequenceGTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21160.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
|| || || || || ||||| ||||| ||||| ||| | ||||| | ||||||||||||||||| |||||||| ||||||||||| || ||| |||||| | || | | | | | |||||| || || ||| | ||| | || | || | | | | ||| | ||
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc-------------tcatgacttctattgttgaatttctgctgagtaacatt-tgtctgacaactgttcttgg-aacatttgcctttag-------------------------------------
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
||||||| ||||| ||||| ||||| ||||| |||||||||||| |||| |||||||||||||| ||||||||||| || |||||||| ||||||||||||| || | | | ||| | ||| || || ||| ||||| | | | | | | | | | || | | | ||| || || ||||
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatt------tcacatctaataatgt----gtttttgt---ttgcattat-------tattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct---------------
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA07G02290.1 (Glycine max), 5'ss of exon 12
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
||||||| ||||| || || ||||| ||||| |||||||||||| |||| |||||||||||||| || |||||||| || |||||||| ||||||||||||| | | || |||| ||| | | || ||| || ||| || ||| ||| | | | | | | || | | | ||||| || ||||
TCTAACTGGCAACAAAACGTACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGGATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagc-------aaac-ctcaatt-----tcacatc-taataat----gtgtttttgtttacattattattgtttctgtgtaa--agtacatcctatcaaaagttagatcatttgttct---------------
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA17G06600.1 (Glycine max), 5'ss of exon 13
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
|| ||||||||||| ||||| ||||| ||||| |||||||| ||| |||||||||| || || || || || ||| | ||||||||||| | || |||||||| | | || | | || || | || ||| ||| || | |||||| || | ||| | | || | || || ||||| ||
TTTCACTGGAAACAAAACATACCAAGAATGGGGTTGGAATATTTTTCAAGCATTTGAAAACAATTCTCGGATTGAGACAGGATATGTTGGACTCAAAGATgtaagaaattcataaac-----------tgcttcaatattttctcctacatgatttac----tctcattctcaaccctgaaaaagttgt-gcatgcatttg-tgaagtattctcata------------------
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 5'ss of exon 8
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
|||||||| | ||||||||| ||||||||||| ||||| |||||| |||||||||| |||||||| ||||||||||| ||||||||||| |||||||||||||| | | || | || ||| | | | || | ||| ||| ||| | | || || || | | || | || |||| |
TTTAACTGGCAGCAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATATGTTGGACTGAAGGATgtaagtacactcttcaaactca-ctaatccctacttc-----agactggctgatttgcatt-------tttagtatttacttttgaactttgattcctgaaatcttagaacat----------------------
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 5'ss of exon 13
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
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TTTAACTGGCAACAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacactcttcaaactca-ctaatccctac----ttcagact------gactgattcgcat--ttttagcatttacttttgaactttgattcctgaaatcttagaaaat----------------------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|125251377|gb|EL265462.1|EL265462EST: CATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGAT GTTAATACAGGCG
genomic: CATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttc ... tcatttccagGTTAATACAGGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG