Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcatttctaatttgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
gtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcatttctaatttgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
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-----------------------------------------------------gcataattgatttcttttcttc--tccagattttgaagaaaatattcctttttcaaaattttc----taataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
---------gtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcatttctaatttgcacgagt--ttgatt---tgagtttatattgtgagcaatgttcattgttctt------ttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
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gtaaattatgttgattt-tatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
gtaag----ttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaatt--ttctgcatttctaatttgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
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gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 18
gtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcattt---ctaatttgca-cgagtttgatttgagtttatattg--tgagcaatgttcat-tgtt--cttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
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-----------------------gttgtatttttaataacatgaattttgaaaattcattcattatgttcgttacatttagactcggttacgtcaagtttaatttacagatgcactaactagaacatgttcatatgttaaccaatgcagGCTATTGCTGAGGAATCACATAGTGAGTCCAAGTGGAAGCAACTGGGAGAATTGGCAATGTCAGCTGGAAAGMapped 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|151411223|gb|EV281034.1|EV281034EST: ACTATAGGTTTGATCTAGCCATACAGCTTGGAAGATTAGAGGTTGCTAAG GGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAA
genomic: ACTATAGGTTTGATCTAGCCATACAGCTTGGAAGATTAGAGGTTGCTAAGgtaagttcat ... tcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
gtttgat putative branch site (score: 5)
ttcattgttctttt putative PPT
atttgagtttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcatttctaatttgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA