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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttaaatctctgtttgataacgtcattagcttgaaattacaaactgtttggaatgcagaatgatcttgatatgaccagaagtacctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC

Basic information

species Oryza sativa
transcript LOC_Os03g57690.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57690.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G899851_T01 (Zea mays), 3'ss of exon 5
-------------------------------ggtttaaatctctgtttgataa--cgtcattagcttgaaattacaaactgtttggaatgcagaatgatcttgatatgaccagaagt--acctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
                                 |||  || | || ||   ||  |      | ||   | | | ||  || |  || || |||   ||  ||  | |   |    |  |  |  |  |||  |||||||   ||||||||| || || ||||| ||||| |  ||||| ||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||
gtaagtactaataaactagagttaatgttgaaatttttatttttgattaccaatccactgccaactaatattcataatgtgatcagattg-agacaaattgtgcaacggataactatcaattttctctttgttagGTTGCATGTGCATGTGCAGTTGCTGCATTGAAGCTACAACGTCCAGTTCGGATGTACCTCGATCGCAAGACAGACATGATAATGGCAGGCGGGCGGCATC

upper sequence: LOC_Os03g57690.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------ggtttaaatctctgtttgataacgtcattagcttga------aattacaaactgtttggaatgcagaatgatcttgatatgaccagaagtacctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
                                              | ||| |||  |   |  ||       | | ||| |       |  | |||    |||  ||||| |  |   | || |||| ||    |   |  |  ||| |||  |||   |||||||||  | || || ||||||||||||||||| ||| | |||||||||||||||||||| |||||||| ||||| |||||| | ||||
gtaagtcctgcctgtaactagagcttcagttcactcaatattttgtgttttcaattgccactgtattgtcaattgaacttcatgatttgaccaaaaaactgttgagatgcaaatggtgttagaaatgatcatggat-tttcctctttgtcagACTGCATGTGCATGTGCCCTTGCTGCCTTCAAGCTGCGGCGTCCAGTTAGGATGTACCTCGATCGCAAGACGGACATGATAATGGCTGGAGGGAGACATC

upper sequence: LOC_Os03g57690.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 5
----------------------------------ggtttaaatctctgtttgataacgtcattagcttgaaattacaaac---tgtttggaatgcagaatgatcttgatatgaccag-aagtacctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
                                    |||  || |    ||   || ||  |  |   ||| | | |  |   || |  || || ||||  |   || ||| |      | |   | |    || ||||||||   ||||||||| || || |||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| ||||| || || |||||||
gtaagtcttaaaaataactagtgcttatgctcaacttttctattttcagttacgaatgtagtgcgtgcgaactgatattcatgtggtcagattg-agaaaaaatgtgttattatagatgactggatttcctctgtcagGTTGCATGTGCATGTGCGGTTGCTGCATTCAAGCTGCGGCGTCCAGTTCGGATGTACCTGGATCGCAAGACAGACATGATAATGGCAGGCGGTCGGCATC

upper sequence: LOC_Os03g57690.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019799_T01 (Zea mays), 3'ss of exon 5
ggtttaaatctctgtttgataacgtcattagcttgaaattacaaactgtttggaatgc-----agaatgatcttgatatgaccagaagtacctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
    ||| ||     |   ||  |   ||   |   ||  |    || |||| | |||     | | ||       |  ||    ||| | ||  | |||| ||| ||||   |||||| || || |||||||||||||| | |||||| |||   |||||||| ||||||||||| |||||||| || ||||| ||||| || |
---gtaagtcataactaactagagcttttctttgctaaacatcgtctatttgtattgccatccaaagtggatgatgtgagatgccaagaatctcctccttgtcagATTGCATGTGCATGCGCCGTTGCCGCATTCAAGCTACAGCGTCCTGTTAAGATGTACCTTGATCGCAAGACGGACATGATAATAGCGGGTGGGCGACACC

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|87023610|gb|CI286361.1|CI286361
EST:     CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACAT                         GTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|29672952|gb|CB669227.1|CB669227
EST:     CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACAT                         GTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|58688136|gb|CK076823.1|CK076823
EST:     CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAACAATGCAT                         GTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGATTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|29646620|gb|CB651627.1|CB651627
EST:     CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACAT                         GTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|29675814|gb|CB672089.1|CB672089
EST:     CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACAT                         GTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|58592575|gb|CF990883.1|CF990883
EST:     GAGAAGAGTTGGAGGAGGTTTTGGTGGGAAAGGCAATGAAAACAATGCAT                         GTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGATTCGA
genomic: GAGAAGAGTTGGAGGAGGTTTTGGT-GGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|218499295|gb|FG965742.1|FG965742
EST:     GCAATGAAAACAATGCAT                         GTTGCCGCTGCAT-T-CTGTCGCCGCA-TCAAGCTGCGGCGTCCGATTCGA
genomic: GCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA
EST: gi|218480859|gb|FG967912.1|FG967912
EST:     CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAACAATGCAT                         GTTGCCGCTGTATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGATTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGA

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: 75 (upstream exon), 71 (downstream exon)
Score: 37

TACTGTTGCGAGGTGCCTTGGCATTCCATATCACAATGTCCGTATCATCACGAGAAGAGTTGGAGGAGGTTTTGGTGGAAAGGCAATGAAAGCAATACATgtgagcatct ... tgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttggaatgcagaatgatcttgatatgaccagaagtacctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
                    tcttgat  putative branch site (score: 37)
                      ttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttaaatctctgtttgataacgtcattagcttgaaattacaaactgtttggaatgcagaatgatcttgatatgaccagaagtacctgttgcttgacagGTTGCCGCTGCATGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - -ctgtttg
- - - - - - - - - - - - - - - gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacctg