Sequence
atgc intronic sequence ATGC exonic sequence...ccgggttcttgtgttttcttttggaagtatctatttttttttttaatttgaatgaagtcaagtgtaatttttatttcatttatctctttcctgggtttagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
Basic information
species | Glycine max |
transcript | GLYMA05G09360.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 6
-ccgggttcttgtgttttcttttggaagtatctatttttttttttaatttgaatgaagtcaagtgtaatttttatttcatttatctctttcc-tgggtttagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
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atttga--caggagagagacttcagtagtggatatttcttcttatggcattgttttccttactgttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
ccgggttcttgtgttttcttttggaagtatctatttttttttt-taatttgaatgaagtcaagtgtaatttttatttcatttatctctttcctgggtt--tagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
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ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattaca---aatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 5
ccgggttcttgtgttttct-tttggaagtatc---tatttttttttttaatttgaatgaagtcaagtgtaatttttatttcatttatctctttcctgggttt----agGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
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--------ttatgttttatgctctgacttatcacacttttgttctgtcatctaaaattgtgttttatatggtttattttactttaactttggtcttgtcctttcacagGTTCAGCTGATAGAACTGTTAAATTCTGGGACCTTGAAACTTTTGAGTTGATTGGTTCAGCTGGACCTGAGMapped 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|207836844|gb|GD807961.1|GD807961EST: TATAGATTTTCATTCCCAATGAGTTTCTACTAGCAACAG GCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTA
genomic: TATAGATTTTCA-TCCCAATGAGTTTCTACTAGCAACAGgttagtctta ... ctgggtttagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgaatgaagtcaagtgtaatttttatttcatttatctctttcctgggtttagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
ttttaat putative branch site (score: 3)
tttttatttcatttat putative PPT
tgtaatttttatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgggttcttgtgttttcttttggaagtatctatttttttttttaatttgaatgaagtcaagtgtaatttttatttcatttatctctttcctgggtttagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - tcttgtg
- - - - - - - - -cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagtgt