Sequence
atgc intronic sequence ATGC exonic sequenceTGAGAAAGGTGTGGATGGTTTATTTGATAGCTTTGCTAGGTTGGATTCCCGTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAGgtaatcttctcttactcaatatctatgactgcaattgttacatatactcactgatcgtgacattactctttgatataatttatcggaacttgcttagttttcatactgaacatttgttttctcatttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13590.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G01660.1 (Glycine max), 5'ss of exon 4
TGAGAAAGGTGTGGATGGTTTATTTGATAGCTTTGCTAGGTTGGATTCCCGTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAGgtaa-----tcttctcttactcaa-tatctatgactgcaattgttacatatactcactgatcgtgacattactctttgatataatttatcggaacttgcttagttttcatactgaacatttgttttctcatttttag-------------------
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AGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCCAGgtagagagttcttccattagtctactatgtttgatggatggattttgatctcacatttgtttgtattatta-tgttttata-ggttggtcggttactcctttgtctttgaaatata-atctcttttctaatttctaattctgttatattttttcag
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G05160.1 (Glycine max), 5'ss of exon 4
TGAGAAAGGTGTGGATGGTTTATTTGATAGCTTTGCTAGGTTGGATTCCCGTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAGgtaatc--ttctcttactcaatatctatgactgcaattgttacatata---ctcac---tgatcgtgacattactctttgatataatttatcgga-----acttgcttagttttcat--actgaacatttgttttctcatttttag-------------------
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AGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCAAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCCAGgtagagagttcttccatgcgtcaactatgtttg--atggatgcatttcgatctcacatttgtttgtattattattatgttttatgttttataggttggtcagttactcctttgtcgttgaaatataatcacttttctaatttctaatcctcttatattttttcag
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 5'ss of exon 4
TGAGAAAGGTGTGGATGGTTTATTTGATAGCTTTGCTAGGTTGGATTCCCGTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAGgtaatcttctcttactcaatatctatgactgcaattgttacatatactcactgatcgtgacattactctttgatataatttatcggaacttgcttagttttcatactgaacatttgttttctcatttttag
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GGAAAAAGGTGTAGATGGTTTGTTTGATAGTTTTGCAAGGTTGGATTCCCGTATTTCAAGTGTTGGACAGACTGCTGCAAAAATTGGAGATCATCTGCAGgta---------tagtc--tatctatgcctgatgttgatacataag------gagaaagacattg---tttgattcaatt-gtatggtgtcctttaatttatacaat-----tctttcttgtcag------Mapped 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|58677372|gb|CK066059.1|CK066059EST: GTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAG AGTGCAGAATCCCAGAGGGAAACTGCTAGTCAGACAATAGATCTCATCAAG
genomic: GTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAGgtaatcttct ... tcatttttagAGTGCAGAATCCCAGAGGGAAACTGCTAGTCAGACAATAGATCTCATCAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAGAAAGGTGTGGATGGTTTATTTGATAGCTTTGCTAGGTTGGATTCCCGTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTACAGgtaatcttctcttactcaatatctatgactgcaattgttacatatactcactgatcgtgacattactctttgatataatttatcggaacttgcttagttttcatactgaacatttgttttctcatttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC