Sequence
atgc intronic sequence ATGC exonic sequence...tgtagtttttagccgaattattaactataactataactcaacttttcactttcatttcctttagaagtatagttgatatatattatatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATTATTGTTGTGGCTGCCGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
Basic information
species | Glycine max |
transcript | GLYMA08G18580.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------tgtagtttttagccgaattattaactataac-tataactcaact-tttcactttcatttcctttagaagtatagttg-atatatatta----tatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATTATTGTTGTGGCTGCCGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
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gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
upper sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0027g00130.t01 (Vitis vinifera), 3'ss of exon 3
-tgtagtttttagccgaattattaactataact-ataa-ctcaacttttcactttcatttcctttagaagtatagttgatatatattatatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATTATTGTTGTGGCTGCCGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
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aaccatcattttaccatttttctaatggccttttataaactcaattttgagcttcaatttccttgcttgagataattc---tattatgtcctcccctttgaagGCGTTTGGGGCGATGAGAGCTCGTGGAGCAAGGGTTACCGACATTGCTATTATTGTTGTGGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAGGCCAMapped 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|193583178|gb|FK540156.1|FK540156EST: TGGATGGGAAAAAGTTGCCGTGTGTTTTCCTTGACACTCCTGGGCATGAG GCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATT
genomic: TGGATGGGAAAAAGTTGCCGTGTGTTTTCCTTGACACTCCTGGGCATGAGgtatgctcag ... attcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcactttcatttcctttagaagtatagttgatatatattatatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATTATTGTTGTGGCTGCCGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
agttgat putative branch site (score: 5)
cattcct putative PPT
tttagaagtatagttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtagtttttagccgaattattaactataactataactcaacttttcactttcatttcctttagaagtatagttgatatatattatatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATTATTGTTGTGGCTGCCGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatatgc