Sequence
atgc intronic sequence ATGC exonic sequencegtaattacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
Basic information
species | Glycine max |
transcript | GLYMA17G07040.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 10
gtaattacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA--------------------
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----------------------------------------aactttcatcattgattcactgtgctcctttcaactttgaaaaaac--aaatt--actatgcaggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG
upper sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 11
--gtaattacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttg------------ttaactgcttgaaaattga--aatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
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gtagaatgactgaataagacaactcacctgacccctcatggttgatgctccagcatgcaaact-ttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA
upper sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G147500_T02 (Zea mays), 3'ss of exon 11
gtaattacttattagtatcactttccaatttgtatcttttaagtatttg-cagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
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gtaggagcc-actggattgagactataagcatcgtacaattgctatttctcccatacacacttgttttcattacatgatga-taattatttctgatgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCTGAGGCAACTGACCGGGAGCTTGAGCTTGAAGCTCAACTGGTTGAAGCAA
upper sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 12
gtaa-ttacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
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gtaggttgtttttttctacatatttttatctcatatttcctattgataacaaaacctagact--ttttttgtaatatttatttttctg----ctgtatttgaaagGAGCGCATGGTTCAATTACAAGATGCACAGAAAGGGGCAGAGGTTACTTCTGAAGCAACTGAGAGGGAGCTTGAGCTTGAAGCTCAACTTGTTGAGGCACMapped 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|21256921|gb|BQ453809.1|BQ453809EST: CCAGAGATCAAATAGAAGAAAGTCTTCGCAACAAAATGGCTTCTATAAAG GAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCA
genomic: CCAGAGATCAAATAGAAGAAAGTCTTCGCAACAAAATGGCTTCTATAAAGgtaattactt ... aaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
tgttaac putative branch site (score: 2)
ttgaaaattgaaatat 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
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gtaattacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
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