Sequence
atgc intronic sequence ATGC exonic sequence...gtgtttattgtgtatagttccaaactagatatgtaaattctatcttcttttttttttatccagattgatcgctttggacattttaaactgtggcatgcagGAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTTTGCCTTGCAAACTTACGGGAACTATTTCATCTACAATGGAGACTGTTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g39010.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g39010.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G060762_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------------------gtgtttattgtgtatagttccaaac-tagatatgtaaa-ttctatcttcttttttttttatccagattgatcgctttggacattttaaactgtggcatgcagGAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTTTGCCTTGCAAACTTACGGGAACTATTTCATCTACAATGGAGACTGTTGG
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gtatgcgcctagaaataacatgatttatttattagaagttgcaataaaataacatttaattgattctccttttagccacaacaagctagattcatttttaacatttactgtgcatgattctgggggtagatatatgaagttatgatcataccatttctgttccagATGGATCGCTTTGGGCATTTCAAACTGTGGCATGCAGGAGGATCTATTTTAGTGGCAATTTCCTTCTCGTCTGTTTTTGGTAGCTGTGTTCCTTGCAAAC-------------------------------------
upper sequence: LOC_Os07g39010.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G121458_T02 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------------gtgtttattgtgtata--gttccaaac-tagatatgtaaa-ttctatcttcttttttttttatccagattgatcgctttggacattttaaactgtggcatgcagGAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTTTGCCTTGCAAACTTACGGGAACTATTTCATCTACAATGGAGACTGTTGG
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gtatgagccaggaaatagcttgattaatttattagaatttgcaataaaataatatgtaatttattctccttttgatcacaataagctaattcatcttagcgtttactgtgtatatgattctgggggtagatatatgaagttatgaacatgcggtttctgtttcagATGGATCGCTTTGGACATTTCAAACTGTGGCATGCAGGAGGATCTATTTTAGTGGCAATTTCCTTCTCGTCTGTTTTTGGTAGCTGTGTTCCTTGCAAAC-------------------------------------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|29655796|gb|CB652071.1|CB652071EST: TTTCTGGTCAATTGGCAGATGGCTTCGCAACAATCTTCGGTGGAGAACTG GAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTT
genomic: TTTCTGGTCAATTGGCAGATGGCTTCGCAACAATCTTCGTTGGAGAACTGgtacgaccta ... tggcatgcagGAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttttttttatccagattgatcgctttggacattttaaactgtggcatgcagGAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTTTGCCTTGCAAACTTACGGGAACTATTTCATCTACAATGGAGACTGTTGG
gattgat putative branch site (score: 4)
tttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttattgtgtatagttccaaactagatatgtaaattctatcttcttttttttttatccagattgatcgctttggacattttaaactgtggcatgcagGAGGATCCATTTTAGTAGCAATTTCCTTCTCATCTGTTTTTGGTAGCTGTTTGCCTTGCAAACTTACGGGAACTATTTCATCTACAATGGAGACTGTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - atatgta