Sequence
atgc intronic sequence ATGC exonic sequencegtaagctggcttcatatatgctcctttgggacagcatgattttataacttggattaactaataaattttgtcttatttttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTGTGTCATCGCTACAATGGATTGTGATGATAGGTTAATTGGTCATGTTGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g04980.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 6
gtaagctggcttcatatatgctcctttgggacagcatgattttataacttggattaactaataaattttgtcttatttttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTGTGTCATCGCTACAATGGATTGTGATGATAGGTTAATTGGTCATGTTGGA
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gtaagctgtctccttttgagctcccttgg------atgattttggaacttggcttgg-tgacatttactgtttcaatttct--atagATGCTTTGGTGGTGAAGTTCTTGAAGGCTATGGAATGACGGAGACATCCTGTATCATATCTGCAATGGATATTGGTGACAGATCAATTGGTCATGTTGGA
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 15
--------------------------------------------------------------------------------------------gtaagctggcttcat-atatgctcctttgggacagcatgattttataacttggattaactaataa-attttgtctt----------attttttta-acagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTGTGTCATCGCTACAATGGATTGTGATGATAGGTTAATTGGTCATGTTGGA
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gtaagttgattattcttctgaggataatgcattattgcatggttgcttgtttaaaagttgtgataaatccattattccacagttacctgtttaaaagttattgttattgtttcttgttttctagaaggaaaaacaaaatatcagtagtgactaattatgttttattgttccataatgaatgtacccatacagATGCTTTGGTTGCCAAGTAATTGAAGGCTATGGAATGACCGAGACCTCTTGTCTCATAAGCTGTATGGATAAGGGTGACAACTTATCTGGTCATGTTGGAMapped 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|29679209|gb|CB675484.1|CB675484EST: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGT ATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTG
genomic: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGTgtaagctggc ... tttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTG
EST:
gi|29671403|gb|CB667678.1|CB667678EST: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGT ATGCTTCGGTTGT
genomic: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGTgtaagctggc ... tttttaacagATGCTTCGGTTGT
EST:
gi|29679207|gb|CB675482.1|CB675482EST: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGT ATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTG
genomic: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGTgtaagctggc ... tttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTG
EST:
gi|109974356|gb|DT806865.1|DT806865EST: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGT ATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTG
genomic: TCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGTgtaagctggc ... tttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTG
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:
52 (upstream exon),
45 (downstream exon)
Score:
9TGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGTGTGAGGCTTATGTCTTCAGGTGCTTCTCCATTGTCAGCAGATGTCATGGAATTCCTAAGAGTgtaagctggc ... tttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTGTGTCATCGCTACAATGGATTGTGATGATAGGTTAATTGGTCATGTTGGA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcatgattttataacttggattaactaataaattttgtcttatttttttaacagATGCTTCGGTTGTCTCGTAATTGAAGGATATGGAATGACAGAGACATCCTGTGTCATCGCTACAATGGATTGTGATGATAGGTTAATTGGTCATGTTGGA
aactaat putative branch site (score: 9)
ttttgtcttatttttt putative PPT
ttggattaactaataa TA-rich tract