Sequence
atgc intronic sequence ATGC exonic sequencegtaactcatccacatgtatagatatttttgtttgtgcagaactgtgcaatcaatactctgacattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g12110.1 (Oryza sativa), 3'ss of exon 4
-----------------------gtaactcatccacatgtatagatatttttgtttgtgcagaactgtgcaatcaa-tactctgacattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
| | | | ||| | |||| | || |||| | | | ||| | | | | | |||||||||| |||||||||| |||||||| ||||| ||||||| || || ||| ||||| || ||||||||||||| ||||||||||| || || ||
accaaattttgggctatttctgtattattgtcttctcaatggtgatcatactgttacataacaatcttgcatttatctgttctaatggct-acctt--tgtagGTCATATTGAATGATCCTTTCCTTGGAAAGCGCATTGAGGAAGGGAATTTTGTCACTGTTCCTTTGAGAGATGAATTCCTTGAAAATGCTCGTCTGTTTA
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G038313_T01 (Zea mays), 3'ss of exon 4
-----------gtaactcatccacatgt-----atagatatttttgtttg-tgcagaactgtgcaatcaatactctgacattttaacat-----gatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
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agcattatcctccattcctcccaaaaatcagcaataataattgttatatgctataaagttgt-taatgtacattatcatgttctaatgtctacttttctagGTTATACTGAATGATCCTTTCCTGGGCAAGCGCGTTGAAGAGGGAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTA
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------gtaactcatccacatgtatagatattt-ttgtttgtgcagaactgtgcaatcaatactctg---acattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
|| || || | | || | || || | | | | | | || | | ||| | || || |||| | | ||| |||| ||| | |||||||| ||||||||||| ||||||| || | |||||||||||||||||||| || ||||| || ||||||||||| | |||||
gtaagcttgctttaatatatgtcaactgtaggagtgatgtaactttggtggtttattcagttctcctttatcttata-atacgtgtccatgttagctactagcactgtaatgggttgtttatattatgcttacctttttaaaatatgcagGTGATTCTCAATGATCCCTTCCTTGGCAAAAGAGTTGAAGAAAGCAACTTTTCAACTGTACCACTAAGGGATGAGTTCCTTGAAAATGCTAGGCTATTTA
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------gtaactcatccacatgtat-agatatttttgtttgtgcagaactgtgcaatcaatact---ctgacattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
||| ||| | | || || | || | | | | || | | ||| | || || ||| | ||| ||||||| | |||||||| |||||||| || ||||||| || | ||||||||||||||||| || || ||||| || ||||||||||| | |||||
gtaagcttgctttaatatatgtcaactataggagtgatattacttttgtggtttatccagttctcctttatcttataatatatctgttcatgttagctactagcgta-gccccgtaatgggttgtttatattatgcttaccctttttaaaaatgcagGTCATACTTAATGATCCCTTCCTTGGTAAAAGAGTTGAAGAAAGCAACTTTTCAACTGTACCGCTAAGGGATGAGTTCCTTGAAAATGCTAGGCTATTTA
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtaactcatccacatgta--tagatatttttgtttgtgcagaactgtgcaatcaatactctgacattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
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ttaacattttgtacaattggataatcattggactatagcttaagtctgatatttcaatgcatccttgcatcaattatgatgacatattattttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTTTCTACTGTGCCATTGAGGGATGAGTTTCTCGAAAATGCCCGGCTTTTTAMapped 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|125047930|gb|EL120199.1|EL120199EST: AAGAGTGTGAAGAG GTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTT
genomic: AAGAGTGTGAAGAGgtaactcatc ... catgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgtttgtgcagaactgtgcaatcaatactctgacattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
ttttaac putative branch site (score: 2)
attttaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactcatccacatgtatagatatttttgtttgtgcagaactgtgcaatcaatactctgacattttaacatgatgtagGTCATTGTGAATGATCCATTCCTTGGCAAGCGAGTTGAGGATGGAAACTTTTCAACTGTACCACTGAGAGATGAATTTCTTGAAAATGCCCGCCTATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG