Sequence
atgc intronic sequence ATGC exonic sequencegtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55490.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 9
----------------------------gtaaactaaaa--actatttaagtt--tcctttgtctgatta-------agatgtg-tttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
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gtataataagaaatggacaaaatgccatgttatctgtatctgttctttttcttggttctttgtttggaaagatagatagatgtggttatgtgggtcgtaatccaagtt--ttgt-tacttttgatagGTGGGAGCACAAACAGAGACCGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCTACCAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 8
---------------------gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagtta----agctcgt-tatg-tattggttaa-agGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
| || | | | || || ||| ||| |||| | |||| ||| || | | | | || | |||| ||| || | |||| ||||||||||| || || ||||| ||||||||||||||||||||||| ||||| || |||||||| |||
gtaatgtgaagtccacgggtcgcaatgtgttatttgttcaatgttcttttcatcgattcaa---tgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 3
----------gtaaactaaaaactatttaagtttcctttgtctga------------ttaagatgtgtttcagagatattaagt-----taag-ctcgttatgtattggttaa-agGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
||| || | || |||| || | ||||| || | | |||| | ||| | | |||| | | || ||| | | |||| ||||||||||| || || ||||| |||||||||||||| |||||||| ||||| || |||||||| |||
gtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctt-tgtctgattaagatgtgtttcagag-atattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
|||| | | | | || | | | | | | | | | | | || | |||| || || | || | || ||||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| ||||||||||| ||||||
gtaac---agactcactgaaatgtggtaatatattagtttggtactctgcaaggtatatcaacttggggcaatttttgtacatatatagGTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtt-tcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
| | ||| | | | | | | | | | | | | | |||| || || || || |||| || ||||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||||
----gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgt-gtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagt-taagctcgttatgtattgg----ttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
||||| | | || | |||| || | | | | | | | || | | ||| | | |||| |||| || |||||||||||||||||||||||||| || ||||| ||||| ||||||| ||||| ||||| |||||||| |||
gtaaattcttagttagtccagttaaaatt-tataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
||||||| |||| ||| || || | |||| || | | |||| |||||||| |||||||||||||||||| | ||||| |||||||| ||||| ||||||||| | ||||| || |||
----------------gtaagtttattttgcagtatt---------tttagcagcacatctttaacttctctgtaaattg----aagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
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----------------gtaagtttattttgcagtatt---------tttagcagcacatcgttaacttttctgtaaattg----aagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAGMapped 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|125224063|gb|EL238148.1|EL238148EST: AGTTGCTGTGATTCAG GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAA
genomic: AGTTGCTGTGATTCAGgtaaactaaa ... ttggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAA
EST:
gi|47832210|gb|CK121894.1|CK121894EST: AACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG GTTGGAGCACAAACTGAGACAGAACTCAA
genomic: AACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaa ... ttggttaaagGTTGGAGCACAAACTGAGACAGAACTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
gtctgat putative branch site (score: 4)
agatattaagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG