Sequence
atgc intronic sequence ATGC exonic sequencegttagcttggttgatatctttttgttcttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
Basic information
species | Glycine max |
transcript | GLYMA11G15010.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
gttagcttggttgatatctttttgtt-cttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
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gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgtt--------cttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 2
gttagcttggttga-tatctttttgttcttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
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----gtggggttgagcaaccattgaattctagggtctatgctatcatgctatgggtcttgtcttgcagacattttggatgtt----gactttgttcttttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
gttagcttggttgatatctttttgttcttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgt-gatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
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-----ctaggtttgtggggctgagca---aacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagcttggttgatatctttttgttcttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
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---------gtt--tgcattgaaattccta----tccgatacaatagtagttta---tgcgcgatttgattaagtactgatgttta----tattttt-ttttaccagGTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------gttagcttggttgatatctttt-tgttcttagttttgaaatttattagtt-attcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
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gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGMapped 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|22525432|gb|BU084243.1|BU084243EST: TTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGNNNNNNNTGAG GTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGA
genomic: TTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAGgttagcttgg ... gtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGA
EST:
gi|18040716|gb|BM309010.1|BM309010EST: TTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGNNNNNNNTGAG GTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGA
genomic: TTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAGgttagcttgg ... gtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
atataac putative branch site (score: 3)
atataacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcttggttgatatctttttgttcttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA