Sequence
atgc intronic sequence ATGC exonic sequence...gtattatatgcacaactgtaggtgcctagccatctgtttgatccctatagtttcatcttgaatttggagaaacttatgcggcctgtttaatctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g15840.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G049190_T01 (Zea mays), 3'ss of exon 10
-------gtattatatgcacaactgtaggtgcctagccatctgtttgatccct---atagtttcatcttgaatttggagaaacttatgcggcctgtttaatctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
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caccatcgacaactaacttttactttggatgtttggtcatctgtttgaccattgcaatggtttgatcttcaaactagaaatatttacattggacat----------gcagGTCCGAGTTGGAAAAAATGTTCACGGGCATGCCTGCAGTTTTTACCGGAATGCTCCAAGGTGAGGAGCTCTCACAAGCGTACGCCAGTGGAGATGTATTT
upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G117153_T01 (Zea mays), 3'ss of exon 10
gtattatatgcacaactgtaggtgcctagccatctgtttgatccct----atagtttcatcttgaatttggagaaacttatgcggcctgtttaatctttg---gcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
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------aatttata-ctttaggtgtttggtcatctgttttgacccttgcaatggtttgatcataataacagaaatatttacattgtctgttttacttgggcatgcagGGCTGAGTTGGAAAAAATGTTCATGGGCATGCCTGCAGTTTTTACCGGAATGCTCCAAGGTGAGGAGCTCTCACAAGCGTACGCCAGTGCGGATGTATTT
upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0007g01940.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------------------------------------------gtattatatgcac--aactgtaggtgcc-tagccatctgtt-tgatccctatagtttcatcttgaa-tttggagaa---acttatgcggcctgtttaatctttgg-cagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
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gtatgttcttttgacatttaatgaggtacttattttctaaaattagttaaagaggccaatctctgagacaaccttggtataattctcatcgagttattcctcttatgaaaatctaccatgagcttcatagtacggtcaagaaacctgcagtttttatttacaaaacatgccttctttctgggcagGGAGGAGCTGGAGAAAATGTTCTCTGGCATGCCTGCTGTGTTCACAGGGATGTTGCAAGGTGAGGAGCTCTCTCAGGCATACGCCAGCGGGGATGTTTTT
upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ29760 (Selaginella moellendorffii), 3'ss of exon 10
gtattatatgcacaactgtaggtgcctagccatctgtttgatccctatagtttcatcttgaattt---ggagaaacttatgc-ggcctgtttaatctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
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-------------------------------------------------gtaagtcactgaatttcatggctaaacttgttctagcgagtccacatcgttgcagGAAGGACTTGGAGGAATTGTTCGCGGATTTGCCAGTGGTTTTCACTGGAATGCTTCAAGGAGAAGAGCTCTCACAAGCCTATGCCAGTGCGGACGTGTTCMapped 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|29682747|gb|CB679022.1|CB679022EST: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST:
gi|29682379|gb|CB678654.1|CB678654EST: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST:
gi|9864970|gb|AU100720.1|AU100720EST: TAAGAATTGCTTTTTGTTGGTGACGGACCATACAG GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: TAAGAATTGC-TTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST:
gi|58691923|gb|CK080610.1|CK080610EST: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST:
gi|33794374|gb|CF323073.1|CF323073EST: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
57 (upstream exon),
74 (downstream exon)
Score:
12GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagtttcatcttgaatttggagaaacttatgcggcctgtttaatctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
gtttaat putative branch site (score: 12)
tcttt CT-rich tract
tttaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatatgcacaactgtaggtgcctagccatctgtttgatccctatagtttcatcttgaatttggagaaacttatgcggcctgtttaatctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - tatgcac
- - - - - - - - - - -gtgccta
- - - - - - - - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcggcc