Sequence
atgc intronic sequence ATGC exonic sequence...ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
Basic information
species | Glycine max |
transcript | GLYMA19G38720.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
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-----------------gtactttgtatagcttagttgttttgtta--attacacggatgcccatgaacactc-ctaa------tgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaaagggactaaat---tatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
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-gtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaa-agGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaa--agggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
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-gagatggtctaagtaatttttcca-acagttttacctttgaattcaaacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGGMapped 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|19348880|gb|BM893412.1|BM893412EST: TCTTCGTGAAACACATAAACAACTGGGTTACAAGAGCATACTGCCACAAG GTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGC
genomic: TCTTCGTGAAACACATAAACAACTGGGTTACAAGAGCATACTGCCACAAGgtatgagaat ... ttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGC
EST:
gi|9899090|gb|BE608058.1|BE608058EST: TCTTCGTGAAACACATAAACAACTGGGTTACAAGAGCATACTGCCACAAG GTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGC
genomic: TCTTCGTGAAACACATAAACAACTGGGTTACAAGAGCATACTGCCACAAGgtatgagaat ... ttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaactaaatgaaacaagacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
gactaaa putative branch site (score: 2)
actaaattatttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA