Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctgtgatatcttttatctataccttggttggtcacaatattaccagaaaaagatggtaccttatgctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
Basic information
species | Glycine max |
transcript | GLYMA11G09990.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G09990.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G348666_T02 (Zea mays), 3'ss of exon 15
gtatgtctgtgatatcttttatctataccttggttggtcacaatattaccagaaaaagatggtaccttatgctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
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tcaaatatttaa-agctcccaatcatgcat-acttcgtttttttatttcttgc------tggttctttctgcaattgc--ttataagatac---ccgaattatgaaaatgc----agGTTCTTGTAACAACTTGCGTGGTGATGGCTCCATTTACACCATTCTTTACTGAAGTTCTTTATCAAAATTTGCGGAAGGTGTCAAGTAATTCTGAGGAGA
upper sequence: GLYMA11G09990.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G158627_T03 (Zea mays), 3'ss of exon 2
gtatgtctgtgatatcttttatctataccttggttggtcacaatattaccagaaaaagatggtaccttatg---ctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
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----------------ttatttctatacctttaaatatttaaagatc-ccaatcatgcacacttttttttgtttcttctccagttgcttataagatacttgaat-tatgaaaa--tgcagGTTCTCGTAACAACTTGCGTGGTGATGGCTCCATTTACACCATTCTTTACTGAAGTTCTTTATCAAAATTTGCGGAAGGTATCAAGTAAATCTGAGGAGA
upper sequence: GLYMA11G09990.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G10320.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgtctgtgatatcttttatctataccttggttggtcacaatattaccagaaaaagatggtaccttatgctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
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----------------------gtatactaaaaatagttgcagagatat--attgtttgtggtcaccatgatttgaacacttgt------tatatctaattat-tgtctattttcagGTGCTCCTTACTTCTTGCAAAGTGATGGCCCCGTTTACACCTTTCTTCACTGAAACTTTGTACCAGAATCTGCGGAAAGCGTGTAAAGGTTCTGAGGAAA
upper sequence: GLYMA11G09990.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv05s0102g00100.t01 (Vitis vinifera), 3'ss of exon 15
gtatgtctgtgatatcttttatctataccttggttggtcacaatattaccagaaaaagatggtaccttatgctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
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---------tcattacctatttgaatatgctactttgaaatccttctatt-------gattatcaccctttttagaaaatcttctctactcttattaacatgt-tggtggtttttagGTGCTTTTAACTTCGTGCAAAGTAATGGCTCCATTCACACCGTTCTTCACTGAAGTTCTTTATCAAAATTTACGGAAAGTTTCCAATGGATCAGAGGAAAMapped 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|120493511|gb|EH221678.1|EH221678EST: CTGGGGAAGAAGACTGCAGGATAGCACTATCAACTCTTTACCAT GTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACT
genomic: CTGGGGAAGAAGACTGCAGGATAGCACTATCAACTCTTTACCATgtatgtctgt ... attctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACT
EST:
gi|120496209|gb|EH224376.1|EH224376EST: CTGGGGAAGAAGACTGCAGGATAGCACTATCAACTCTTTACCAT GTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACT
genomic: CTGGGGAAGAAGACTGCAGGATAGCACTATCAACTCTTTACCATgtatgtctgt ... attctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccttatgctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
acttaat putative branch site (score: 4)
ttctttc putative PPT
acttaattatatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctgtgatatcttttatctataccttggttggtcacaatattaccagaaaaagatggtaccttatgctagagcagttgtagagtgtagacttaattatatgaattctttcagGTGCTTTTGTTATCCTGTAAAGTGATGGCTCCTTTTACACCTTTCTTCACTGAGGTGCTCTATCAAAATATGCGAAAAGTTTCTAATGGATCAGAGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA