Sequence
atgc intronic sequence ATGC exonic sequence...ttatactatcttcgtctgaccctgaacgtagtagtatatgcctaataaacttcccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
Basic information
species | Glycine max |
transcript | GLYMA08G46170.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 3
ttatactatcttcgtctgaccctgaacgtagtagtatatgcctaataaacttcccttaacaag-tgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
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-cacagtgctttctaatatttcattccagaacatttaattctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
upper sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G48640.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------------------------ttatactatcttcgtctgaccctgaacgtagtagtatatgcctaataaacttcccttaacaagtgtcaa---ctgatgacta---tcttcattttttcatttga-------agGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
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gtatgcaatgtatttttgatatgatcgtatacatcaatgtgcatctttgtgtatgtgaggaatgaaatgagttaaattcttgtcatgccagtgtctctctatgttgcatctc-tgctatcaaaaacgttaactgtgttacgaaagttttcagttttggtgtctaatatcttccttttgttactatactatctcagAAAGAGTATGGTAGAGTTTGAGCCTCGACTTGTTGCTCTTACGTGCTTGTACCTGGCATCTAAAGCTGAAGAAAGCATAGTGCAGGCCAGGAATCTTGTT
upper sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 4
ttatactatcttcgtctgaccctga-acgtagtagtatatgcctaataaacttcccttaacaagtgtca-actgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
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agatagcattttgagcacttcttctcacaaattaattcaggcagactgtaaaccccggactggatctcttgctaagcttaatttttatttgtgctttc--agAAAAGCTATGACAGAATATGATCCACGTCTTGTGGCTCCAACTAGCTTGTACTTGGCTGCAAAAGCAGAAGAAAGCACTGTGCAGGCTAGACTTCTTGTA
upper sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S18_263V6.1 (Physcomitrella patens), 3'ss of exon 2
ttatactatcttcgtctgaccctgaacgta-gtagtatatgc-ctaataaacttcccttaacaagtgtcaact-gatgactatcttcat--tttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
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gcgtcctgccttgtttagtttcttattctaagttttagttattccaattaattttcgt-----ggtgccattttgttaataatctgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
upper sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S427_18V6.1 (Physcomitrella patens), 3'ss of exon 4
ttatactatcttcgtctgaccctgaacgtagtagtatatgcctaataaacttccctt--aacaag----tgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
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---tgatttcctactactacttcaaa-acaattaggtcagtttagccaatttctcttttgccatggctatatttgccgacaaggagttggattcttttgt--gcagAAAAAGTTTCTCCGAATTCGATCCACGGCTAGTTGCTCCTACATGTCTGTATCTGGCCTCCAAAGCAGAAGAAAGTACAGTGCAGGCTAAGCTTCTTGTTMapped 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|6566336|gb|AW234009.1|AW234009EST: GGTTGTGGCCACAGCAGTTACATACATGAGGCGTGTTTACACCAG GAAGAGTATGGCTGAATATGATCCGCGCTTGGTAGCTCCAACATGCTTGTA
genomic: GGTTGTGGCCACAGCAGTTACATACATGAGGCGTGTTTACACCAGgtatgtgtcg ... tcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTA
EST:
gi|19348833|gb|BM893365.1|BM893365EST: GGTTGTGGCCACAGCAGTTACATACATGAGGCGTGTTTACACCAG GAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTA
genomic: GGTTGTGGCCACAGCAGTTACATACATGAGGCGTGTTTACACCAGgtatgtgtcg ... tcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaacttcccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
aactgat putative branch site (score: 3)
tcttcattttttcatt putative PPT
ttcattttttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatactatcttcgtctgaccctgaacgtagtagtatatgcctaataaacttcccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - -ccctgaa
- - - - - - - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - -cttccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg