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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattactttgatctttaattgcatgctgtcagctcattaaacaaaatgcttcctttcattttcttgtatggtctattcgtcatgttatgatcggacttgttctgtttggatcataccacatcatcatggttttcaactgaagtgtagtttctgttgtattaaatattgtttgacaccattcctgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAACACTCCGAATTTTATCAGAGCCGAGGTACTTCCCAGTGGTTATCTGATTC

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 7
gtattactttgatctttaattgcatgctgtcagctcattaaacaaaatgcttcctttcattttcttgtatggtctattcgtcatgttatgatcggacttgttc-tgtttggatcataccacatcatcatggttttcaactgaagtgtagtttctgttgtattaaatattgtttgacaccattcctgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAACACTCCGAATTTTATCAGAGCCGAGGTACTTCCCAGTGGTTATCTGATTC
                                                                                          | ||   |  ||  || |||| |   ||  | |   | || |  | |  |    || |  | |||  ||| |    |   | || | |  ||    |||| |||||||| |||||||||||||||||||||||||| || || ||||| ||||||||||| |||||||||||||| ||||| ||||| ||||||||||||||||
----------------------------------------------------------------------------------------ccagcgtgttaattgatgcttggcttccacttcttttgcttgatcattatatttgatgca--tactgcagtactggtaacactgtggctctgtt----ttctctagATCTGCGAAAGGTCATTGACTCAGTCCACTGGAGGTCCTTCTGGACCTAACACTCCAAATTTTATCAGAGCTGAGGTGCTTCCTAGTGGTTATCTGATTC

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 6
gtattactttgatctttaattgcatgctgtcagctcattaaacaaaatgcttcctttcattttcttgtatggtctattcgtcatgttatgatcggacttgttctgtttggatcataccacatcatcatggttttcaactgaagtgtagtttctgttgtattaaatattgtttgacaccattcctgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAACACTCCGAATTTTATCAGAGCCGAGGTACTTCCCAGTGGTTATCTGATTC
                                                                                  |  |  | | |  |||  | |||      |  |    ||| |||||  | ||    ||  |  ||         |||||    |   | || | |  |   | ||||||||||||| |||||||||||||| || |||||||| || || ||||| ||||| |||||  ||||||| ||||| ||||| ||||| ||||||||||||||||
---------------------------------------------------------------------------------gacttagtaaccccactgatgctgcc--atttcttttgcatgatcattatatt----tgctgcataaa----acagtattggtaaccatgtggctc--tctgtcttctgtagATCTGCGAAAGGTCATTGACCCACTCCACTGGAGGTCCTTCTGGACCTAAAACTCCAGATTTTATAAGAGCTGAGGTGCTTCCTAGTGGTTATCTGATTC
















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|58661675|gb|CK050355.1|CK050355
EST:     ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTG                         ATCTGTGAAAGGTCATTGACTCAGTCCACTGGTTGGCC-ATCTGGGCCTAA
genomic: ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGT-GGCCCATCTGGGCCTAA
EST: gi|58654155|gb|CK042835.1|CK042835
EST:     ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTG                         ATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
genomic: ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
EST: gi|58682325|gb|CK071012.1|CK071012
EST:     GTGGACTTGAAGATGGGAGTCTTGTG                         ATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
genomic: GTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
EST: gi|58667004|gb|CK055690.1|CK055690
EST:     ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTG                         ATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
genomic: ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
EST: gi|58675209|gb|CK063896.1|CK063896
EST:     ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTG                         ATCTGTGAAAGGTCATT
genomic: ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATT
EST: gi|58675501|gb|CK064188.1|CK064188
EST:     ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTG                         ATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC
genomic: ACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAAC

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: 47 (upstream exon), 62 (downstream exon)
Score: 17

ACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTGgtattacttt ... tgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAACACTCCGAATTTTATCAGAGCCGAGGTACTTCCCAGTGGTTATCTGATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagtgtagtttctgttgtattaaatattgtttgacaccattcctgttctgtagATCTGTGAAAGGTCATTGACTCAGTCCACTGGTGGCCCATCTGGGCCTAACACTCCGAATTTTATCAGAGCCGAGGTACTTCCCAGTGGTTATCTGATTC
                              gtttgac  putative branch site (score: 17)
                                         ttcctgttct  putative PPT
                ttgtattaaatattgt  TA-rich tract