Sequence
atgc intronic sequence ATGC exonic sequence...actaaatttggcaatttttgacttagcaaagttttataaatctatttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaatgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
Basic information
species | Glycine max |
transcript | GLYMA20G23250.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G23250.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 7
actaaatttggcaatttttgacttagcaaagttttataaatctatttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaa-tgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
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gtgaacataaagaactgtttacaggttctctgtttgctact-tatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
upper sequence: GLYMA20G23250.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G029055_T01 (Zea mays), 3'ss of exon 7
-actaaatttggcaatttttgacttagcaaagttttataaatctatttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaatgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
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gagcaacaaatgcatgtagattcccagtcaccttttatgt-tttatctccgcaagtcgcttttatttcatgcaccaatgatttctattttgaaaattctagGATGGCATGAAGATGGGAAAGTCACTAGGCAACACACTTGAACCAAAAGATCTGGTAGAAAGATTTGGTGCTGATGCTGTTAGGTATTTCTTCTTGCGGG
upper sequence: GLYMA20G23250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 3'ss of exon 7
actaaatttggcaatttt--tgacttagcaaagttttataaatctatttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaatgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
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aacaattatagacatgatagtgagttatcagctgttaatat-tttatctcatataccta-ttttatttcatgcagcaatgctttttatttttaaaattttagGATGGAATGAAGATGGGAAAATCATTGGGGAATACACTTGAACCAAATGATTTGGTTCAAAGATTTGGCTCGGATGCAGTAAGATACTTTTTCCTTAGGGMapped 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|120531087|gb|EH259220.1|EH259220EST: CTGGACTAAGCCTTCCTAAAATGGTATTTGGCCATGGATTCTTGACAAAG GATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGAT
genomic: CTGGACTAAGCCTTCCTAAAATGGTATTTGGCCATGGATTCTTGACAAAGgtatttgtag ... aaaatgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaatgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
atttaat putative branch site (score: 4)
tttttattttgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaaatttggcaatttttgacttagcaaagttttataaatctatttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaatgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgca