Sequence
atgc intronic sequence ATGC exonic sequencegtttctttttcactcttcattgctcataattttactgttctcgaatttttaatataaagttttctcttttaccgatatgtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07270.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G38270.1 (Glycine max), 3'ss of exon 1
gtttctt--tttcactcttcattgctcata-attttactgttctcgaatttttaatataaagttttctcttttaccgatatgtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
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gtccctttatttcactttttatatctaatccaatataatctaatgcaaccctttttacttattcatttatttctgttgggttttctgttagATTGTGGCATTGTTGCTGGAGAATGGAGCTGATGTGAATTCCAGAAATTATTGTGGCCAG
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G29590.1 (Glycine max), 3'ss of exon 1
gtttctttttcactcttcattgctcataattttactgttctcgaatttttaatataaagttttctcttttaccgatatgtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
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----------gtccctttatttcactttttttacatctaatccaaccctttaatttatttatttttctctgttggttttc--tgttagATTGTGGCATTGTTGCTGGAGAATGGAGCTGATGTGAATTCCAGAAATTATTGTGGCCAG
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G26560.1 (Glycine max), 3'ss of exon 1
----------------------gtttctttttcactcttcattgctcataattttactgttctcgaatttttaata-------taaagttttctct---tttaccgatatgtgatg---ttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
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gtttcaattctcaatctcaatcacttcttttttttttttcgtttttt-tcattttggtgagtttctgtttttaccggttttcttcgactcccttctgattttgtttatctgggtttctcttagATTGTGGCATTGTTGCTTGAAAATGGAGCTGATGTGAATTCGAGAAATTATTGTGGGCAG
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G32090.1 (Glycine max), 3'ss of exon 1
------------------------------gtttctttttcactcttcattgctcataa-----ttttactgttctcgaatttttaat-ataaagttttctcttttaccgatatgtgat---gttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
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gtttcaattctcaatctcaaccaccccttttttcgtttttctcattttcatgtttgaaagtcttttttttttctcttccgttttcatcgaccccctttttgattttgtttatctgggtttctgttagATTGTGGCATTGTTGCTTGAAAATGGAGCTGATGTGAATTCGAGAAATTACTGTGGGCAG
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtttctttttcactcttcattg-ctcataattttactgttctcg---aatttttaatataaagttttctcttttaccgatat-gtgatgtt-------agATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
| || || | ||| || |||| |||| || | | | | || | | | | | |||| | | | | ||| |||| |||| || | ||| |||| ||||| |||||||||||||||||||||||||| || || |||
gtcgttttccgcttctcactcctttgatactcactgattcatcgtttttttgacccggtaaagtgttgtacttgcgttgattttttttcctggttttgtgttgttgttgagtagATTGTTGCTTTGCTGCTGGAGAATGGAGCTGATGTGAATTCCAGAAATTACTGTGGACAGMapped 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|124917792|gb|EH991666.1|EH991666EST: TCTTAATTCTCCTTTGCATTTCGCTGCAGCTAAAGGCCATAACGAG ATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTAT
genomic: TCTTAATTCTCCTTTGCATTTCGCTGCAGCTAAAGGCCATAACGAGgtttcttttt ... gtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTAT
EST:
gi|164174039|gb|ES166587.1|ES166587EST: TGGTCTTAATTCTCCTTTGCATTTCGCTGCAGCTAAAGGCCATAACGAG ATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAA
genomic: TGGTCTTAATTCTCCTTTGCATTTCGCTGCAGCTAAAGGCCATAACGAGgtttcttttt ... gtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgttctcgaatttttaatataaagttttctcttttaccgatatgtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
ttttaat putative branch site (score: 3)
aatttttaatataaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctttttcactcttcattgctcataattttactgttctcgaatttttaatataaagttttctcttttaccgatatgtgatgttagATCGTCGGATTGTTGCTCGAGAACGGAGCTGATGTGAATTCCAGAAATTATTGCGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT