Sequence
atgc intronic sequence ATGC exonic sequencegttgaaacaaatacatgcattctggtttaactatacttaattcatgctgaatgttagatgcatagaattgtagcacgtcatggtttatgggacatttgtcttacaggaatagcttgctttctacaattgctgctggcaattattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g49010.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g49010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G876520_T04 (Zea mays), 3'ss of exon 2
gttgaaacaaatac-----atgcatt------ctggtttaactatacttaattcatgctgaatgttagatgcatagaattgtagcacgtcatggtttatgggacatttgtcttacaggaatagcttgctttctacaattgctgctggcaattattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
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gtcaagatagctgccctttatgctttaactaactgattttgttttattcacttttcattta-tggcagctacttaaattccagtaaagccattgttcatggcacatatga-tcaatggtgtggcatgctta-tactattgctatggtcagttttgacatgagaagattac------ttatgttcatgttgttttgttacagGGTAAACAGAGGTTGCTTTACAGCTTACTTGATGCAATGCAATCTCTAACATCCCAAGCTGTTGTCATTGGTGTGAGTTGCCGCTTG
upper sequence: LOC_Os01g49010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G25850.1 (Glycine max), 3'ss of exon 8
gttgaaacaaatacatgcattctggtttaactatacttaattcatgctgaatgttagatgcatagaattgtagcacgtcatggtttatgggacatttgtcttacaggaatagcttgctttctacaattgctgctggcaa-ttattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
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---------------------------------------------------------------------------agtaataccctttgtggtctctg--------aaatattttctattaaacattt----ttggcaacttttttaatcatacattcactactatctccatcc-tgatttt---ttgcagGGTAAACAGAGATTACTCTATAGCTTGCTAGATGCAATGCAATCAATAACATCACAGGCTGTTGTACTTGGCATTAGTTGTCGTCTG
upper sequence: LOC_Os01g49010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G41410.1 (Glycine max), 3'ss of exon 7
gttgaaacaaatacatgcattctggtttaactatactt----aattcatgctgaatgttagatgcatagaattgtagcacgtcatggtttatgggac-atttgt--cttacaggaatagcttgctttctacaattgctgctggcaattattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
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gtaaggctcctctttctttttccactttgatcacttctcaaaagcttgtggtgtaaattctgggt-tataattgtagttattctcaacctctaatactgtttgtggtctatgtgaaatattttctattaaacatttttggtaac--ttttttaatcataaatttgctactatctccatcc-tgattct---ttgcagGGTAAACAGAGATTACTCTATAGCTTGCTAGATGCAATGCAATCAATAACATCACAGGCTGTTGTACTTGGCATTAGTTGCCGTCTG
upper sequence: LOC_Os01g49010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv01s0011g04400.t01 (Vitis vinifera), 3'ss of exon 7
gttgaaacaaatacatgcattctggtttaactatacttaattcatgctgaatgttagatgcatagaattgtagcacgtcatggtttatgggacatttgt-cttacaggaatagcttgctttctacaattgctgctggcaattattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
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---------------------------------------------------------------------------------------------gtgtgcacacacacaaaagaaaacccatgtggatcggtttttgacattta--aattctcagac--ataggtattaccagttccctttgttctttgcagGGGAAACAACGATTACTTTATAGCTTGTTGGATGCAATGCAATCTGTGACGTCACAAGCAGTTGTCATTGGTGTCAGTTGCAGACTAMapped 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|218491615|gb|FG954647.1|FG954647EST: CTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG GGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACC
genomic: CTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAGgttgaaacaa ... cctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaattattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
ggataac putative branch site (score: 3)
tttcctatt putative PPT
atgattctatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaaacaaatacatgcattctggtttaactatacttaattcatgctgaatgttagatgcatagaattgtagcacgtcatggtttatgggacatttgtcttacaggaatagcttgctttctacaattgctgctggcaattattagataacaggataacagatgattctatttatggtttcctattacagGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT