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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttatgattttcccatgcataaccgcgaatgccctatggccattgttgttttgtcttgatgtcttgagctcagtctcttactggtttatctggtcttatgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACTAGAGGCCCATCTCCACTTATCAACCAGTGGTTTGACTTCTGCCTGCAGA

Basic information

species Oryza sativa
transcript LOC_Os04g51310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G129071_T01 (Zea mays), 3'ss of exon 5
gtgtgttatgattttcccatgcataaccgcgaatgccctatggccattgttgttttgtcttgatgtcttgagctcagtctcttactggtttatctggtcttatgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACTAGAGGCCCATCTCCACTTATCAACCAGTGGTTTGACTTCTGCCTGCAGA
|| || ||||| |||| |||| ||||       |||   || |||||| |                   || ||     ||||| || |||         ||| |  |  |||| |||||||  || || | |||||||||||| | ||| ||  || || | |||||||| ||||||||  |  |||||||||| ||||||||||||||||
gtatgctatgactttctcatgtataa-------tgc---attgccattat-------------------gaactatacatcttattgattt--------ctataccctgtagGCAATACCATGCGCGACGAGATTTCAGACTGACCAAATCGGGAGCCGAGCCAGAGGCCCGTCTCCACTGGTTCACCAGTGGTTCGACTTCTGCCTGCAGA

upper sequence: LOC_Os04g51310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G455978_T02 (Zea mays), 3'ss of exon 4
gtgtgttatgattttcccatgcataaccgcgaatgccctatggccattgttgttt----tgtcttgatgtcttgagctcagtctcttactggtttatctggtcttatgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACTAGAGGCCCATCT---CCACTTATCAACCAGTGGTTTGACTTCTGCCTGCAGA
                                 |    |||||   |  |  |      ||  |||  || | || ||  |||  ||  || ||  | |||| |||| | |   |||| | |||    || ||   ||| ||||| || | ||| ||  || |||| ||||||||||||   ||||| ||| |||||||||| |||||||||||||   
--------------------------------gtatgttatggttttcctcatccgcaatgcattgtcgtttcgaact--gtccttt--tgattgttatggttttattcgtcgtagGCAACACCGCGCGCCACAGGATTCCAGACCGACCAAATCGGTAGCCGAACCAGAGGCCCATCTTCTCCACTCATCCACCAGTGGTTCGACTTCTGCCTGC---
















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|88413099|gb|CI578950.1|CI578950
EST:     TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACC
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACC
EST: gi|86871031|gb|CI328233.1|CI328233
EST:     TTGCAGTGGT-GTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|29688719|gb|CB684994.1|CB684994
EST:     TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|89187726|gb|CI115172.1|CI115172
EST:     TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|88478679|gb|CI415950.1|CI415950
EST:     GGCTGATGTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: GGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|29659389|gb|CB655664.1|CB655664
EST:     TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|86883654|gb|CI328705.1|CI328705
EST:     GGCACTAGTCTATGGGCTGATCTATGG                         GCCATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: GGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|86836739|gb|CI347361.1|CI347361
EST:     CAAGTCAGCCACGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: CAAGTCAGGCA-GTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|29679485|gb|CB675760.1|CB675760
EST:     TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
EST: gi|89187707|gb|CI115153.1|CI115153
EST:     TTGCAGTGTTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGG                         GCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT
genomic: TTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACT

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: 71 (upstream exon), 58 (downstream exon)
Score: 7

AGTGGGTTGGAGCAGTGATGTTATTCCTGCTGCGAAGCGAATGTCTGACGTTGCAGTGGTGGTTCCCAAGTCAGGCAGTAGTCTATGGGCTGATCTATGGgtgtgttatg ... tgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACTAGAGGCCCATCTCCACTTATCAACCAGTGGTTTGACTTCTGCCTGCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatgtcttgagctcagtctcttactggtttatctggtcttatgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACTAGAGGCCCATCTCCACTTATCAACCAGTGGTTTGACTTCTGCCTGCAGA
                     ctcttac  putative branch site (score: 7)
                               tttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttatgattttcccatgcataaccgcgaatgccctatggccattgttgttttgtcttgatgtcttgagctcagtctcttactggtttatctggtcttatgcattccagGCGATACCATCTGCAACCAAATTTCAGACTGATCGAATTGGCGGCAGAACTAGAGGCCCATCTCCACTTATCAACCAGTGGTTTGACTTCTGCCTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG