Sequence
atgc intronic sequence ATGC exonic sequence...aatttctgaacctattctctatctctgtttctgaaatatgaagagacctctcctatggcatctgggcattattcattcatctttggttgattatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAAGAGAACTTCGGATTCGAAGAAAGGGCATGGAAGCTGTGAAGAAACAAAC
Basic information
species | Glycine max |
transcript | GLYMA09G00790.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G00790.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0116g01280.t01 (Vitis vinifera), 3'ss of exon 1
aatttctgaacctattctctatctctgtttctgaaatatgaagagacctctcctatggcatctgggcattattcattcatctttggttga-ttatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAAGAGAACTTCGGATTCGAAGAAAGGGCATGGAAGCTGTGAAGAAACAAAC
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aatgtgcatttttatttttagcccttttacccttcagcttctaaccccattgccattgcctatgaat-ttgtaatgatgtttttgggggacttacatgcagGATTCACCCTCTTCCTTGCACTAATGATAGACAGACTACATCACTACATCAGAGAACTCCGTTTAAGAAGGAAGAGCATGGAAGCTATAAAGAAACAAAA
upper sequence: GLYMA09G00790.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0116g01260.t01 (Vitis vinifera), 3'ss of exon 1
aatttctgaacctattctctatctctgtttctgaaatatgaagagacctctcctatggcatctgggcat-tattcattcatctttggttgattatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAAGAGAACTTCGGATTCGAAGAAAGGGCATGGAAGCTGTGAAGAAACAAAC
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-atgtgcatttttattttcagcccttttacccttcagcttctaaccccattgccattgcctatgaatttgtatatgatgtttttgggagacttacatgcagGATTCACCCTCTTCCTTGCACTAATGATAGACAGACTACACCACTACATCAGAGAACTCCGTTTAAGAAGGAAGAGCATGGAAGCTATAAAGAAACAAAAMapped 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|192295531|gb|FG988105.1|FG988105EST: CACCGATCAGGTTCTTATGGCCAAGCACCTCCTCGAAGCAACGCTCATGG GTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAA
genomic: CACCGATCAGGTTCTTATGGCCAAGCACCTCCTCGAAGCAACGCTCATGGgtatgtattt ... ttatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAA
EST:
gi|193621257|gb|FK572257.1|FK572257EST: GAAGCAACGCTCATGG GTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAA
genomic: GAAGCAACGCTCATGGgtatgtattt ... ttatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctctcctatggcatctgggcattattcattcatctttggttgattatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAAGAGAACTTCGGATTCGAAGAAAGGGCATGGAAGCTGTGAAGAAACAAAC
ggttgat putative branch site (score: 5)
attattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttctgaacctattctctatctctgtttctgaaatatgaagagacctctcctatggcatctgggcattattcattcatctttggttgattatttgcagGTGCTATCCTTTTCCTTGCGCTTATGATAGACAGACTACATCATTACATAAGAGAACTTCGGATTCGAAGAAAGGGCATGGAAGCTGTGAAGAAACAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -ctgaacc
- - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcat