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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctgttaactgttaccattagtaatgtgttatatgttcttctttgttcaaaataattttgagtataatgcatccgtaatcagtcaaaattgtgtttcctttacaatagaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCAATGAGTTTTGGCTACTGAGAGATAAATTGATAGCACTCAATGAGACTGT

Basic information

species Oryza sativa
transcript LOC_Os04g36050.1
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G016894_T01 (Zea mays), 3'ss of exon 5
gtatcctgttaactgttaccattagtaatgtgttatatgttcttctt-tgttcaaaataattttgagtataatgcatccgtaatcagt-caaaattgtgtttcctttacaatagaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCAATGAGTTTTGGCTACTGAGAGATAAATTGATAGCACTCAATGAGACTGT
          || | | |   ||     ||   | |   | |  ||  |||| |||       |    | ||   |   ||  | ||       |||  |||||||||||||||    |||||| ||||||| ||||||  | |   | | || || || || |||||||||||||||||||||||| |||  |||||||| ||||| |||||         
---------aaaatttcattgtt-----tgaactttgaatccaactaatgttgaaagctggaatatagaaaagttacatgttttgagaatggttttggttttcctttacaatagCTTGACAGATCTGAATGTGGATCCAGTTACGGGCGATTATTATCCTACAGTATTCTTCAATGAGTTTTGGCTATTGAAGGATAAATTAATAGCGCTCAAC--------

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G437119_T02 (Zea mays), 3'ss of exon 6
gtatcctgttaactgttaccattagtaatgtgttatatgttcttctttgttcaaaataattttgagtataatgcatccgtaatcagtcaaaatt-gtgtttcctttacaatagaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCAATGAGTTTTGGCTACTGAGAGATAAATTGATAGCACTCAATGAGACTGT
                   ||||  |    | | | |  ||  |    |     ||||  |   |   | |        || | ||  |   || |  ||||||||||||||||   |||||| ||||||| |||||| || ||  | | || || || || ||||||||||| |||||||||||  |||| |||||||| ||||| ||||||||| ||||
------------------gcattgttcgaat-tcaaactttgctgaaagcctggaata--tagaaaagttacatgcttttagtgagaaaggttttgattttcctttacaatagattgacagATCTGAATGTGGATCCAGCTACAGGCGATTATTATCCTACAGTATTCTTCAACGAGTTTTGGCTTTTGAGGGATAAATTAATAGCGCTCAATGAGTCTGT
















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|58607128|gb|CK035161.1|CK035161
EST:     GTATCCACACAATAATGTTCCACCCAATGTTGCTCCAT                         ATTTGAATGTTGATCCATCTTCAAACAACTACTACC
genomic: GTATCCACACAATAATGTTCCACCCAATGTTGCTCCATgtatcctgtt ... agaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACC
EST: gi|33675031|gb|CF303270.1|CF303270
EST:     GTATCCACACAATAATGTTCCACCCAATGTTGCTCCAT                         ATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
genomic: GTATCCACACAATAATGTTCCACCCAATGTTGCTCCATgtatcctgtt ... agaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
EST: gi|29683509|gb|CB679784.1|CB679784
EST:     GTATCCACACAATAATGTTCCACCCAATGTTGCTCCAT                         ATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
genomic: GTATCCACACAATAATGTTCCACCCAATGTTGCTCCATgtatcctgtt ... agaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
EST: gi|109974448|gb|DT806914.1|DT806914
EST:     GTATCCACACAATAATGTTCCACCCAATGTTGCTCCAT                         ATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
genomic: GTATCCACACAATAATGTTCCACCCAATGTTGCTCCATgtatcctgtt ... agaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
EST: gi|84117031|gb|CD150798.1|CD150798
EST:     GTATCCACACAATAATGTTCCACCCAATGTTGCTCCAT                         ATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA
genomic: GTATCCACACAATAATGTTCCACCCAATGTTGCTCCATgtatcctgtt ... agaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCA

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: 63 (upstream exon), 38 (downstream exon)
Score: 32

GTATCCACACAATAATGTTCCACCCAATGTTGCTCCATgtatcctgtt ... agaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCAATGAGTTTTGGCTACTGAGAGATAAATTGATAGCACTCAATGAGACTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataatgcatccgtaatcagtcaaaattgtgtttcctttacaatagaaatacagATTTGAATGTTGATCCATCTTCAAACAACTACTACCCAACTGTATTCTTCAATGAGTTTTGGCTACTGAGAGATAAATTGATAGCACTCAATGAGACTGT
 ttcctttac  putative branch site 
                                     tttacaatagaaata  TA-rich tract