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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacaccatttcactgtttgcatggtgtgcattgtttttttcacttgattgcttcatctacttatttgtttcatatctttgcatatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA

Basic information

species Oryza sativa
transcript LOC_Os05g37120.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G141735_T01 (Zea mays), 3'ss of exon 13
----------gtaagtacaccat-ttcactgtttgcatggtgtgcattgtttttttcacttgattgcttcatctacttatttgtttcatatctttgcatatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA
| | || || |||| | | | | | ||||| ||| || | || || ||| | | | |||| || ||||| |||||||||| | | |||| ||||||||| ||| |||||||| || ||||| ||||| ||||||||||| ||| ||| || ||||||||||
attaattttcttgaaagtcttatgtttgttgttgagagcataaataggagcaatgttacttgcttgttttagctgctgattc--------tttctacataccatgtagGCCTTTTGAGAAAAACAATAAATGGACTGAAGCAGGACAGATGTATAACCCCCAAGCTTACATTCATCCATGGAGGGAAAGATGATTCAACATTGTTTGA

upper sequence: LOC_Os05g37120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 13
--gtaagtacacc----atttcactgtttgcatggtgtgcattgtttttttcacttgattgcttcatctacttatttgtttcatatctttgcatatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA
| | || | | | ||| |||| | || | || | | |||| | | ||| | | | || | ||| | | |||| || ||||||||||||||||| | | ||| | ||||||||| ||| |||||||| |||||||| ||||| ||||||||||| ||| ||| || ||||||||||
atattaatattcttgaaagtctactttttgt-tattgaggatagataggagcactcg--tacttgcttgtttcagctgctgattatttctacataccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA
















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|396941502|gb|HO188711.1|HO188711
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGATTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|66912670|gb|CX099518.1|CX099518
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGATTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|86437489|gb|CI119211.1|CI119211
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|87037648|gb|CI192270.1|CI192270
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|24208894|gb|AU225921.1|AU225921
EST:     TCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: TCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|29630915|gb|CB635924.1|CB635924
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGATTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|29616494|gb|CB621506.1|CB621506
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGATTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|29674496|gb|CB670771.1|CB670771
EST:     CTATTCACCTTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
EST: gi|58692848|gb|CK081535.1|CK081535
EST:     CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACT                         GTCTTTTGAGAACCATGATTAATGAGTTGAAGCAGGGCAGGTGTATAACAC
genomic: CTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACAC

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: 12 (upstream exon), 66 (downstream exon)
Score: 3

AGTGAGAGCCCCATATTTCTTCTGGATGCATTTACGAACCTTATTGTTTACTATTCACCGTCTGCTGATCCTTCACTTCCTTTTCCTCCACCTCATGACTgtaagtacac ... tatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacttgattgcttcatctacttatttgtttcatatctttgcatatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA
    acttgat  putative branch site (score: 3)
 ttatttgtttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacaccatttcactgtttgcatggtgtgcattgtttttttcacttgattgcttcatctacttatttgtttcatatctttgcatatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA