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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGCACAAGTATACAGCTTTCTGGGAAGCATATTTGATCCAGATACTAGTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttcttgagatttgagatatagtttctgaatgttctatgattatatcgtatccttttcccaacacagatattcttaattttgaagtagcggaaat...

Basic information

species Oryza sativa
transcript LOC_Os06g45840.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 6
TTTTGCACAAGTATACAGCTTTCTGGGAAGCATATTTGATCCAGATACTAGTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttcttgag-atttgagatatagtttctgaatgttctatgattatatcgtatccttttcccaacacagatattcttaattttgaagtagcggaaat--
|||||| |||||||||| ||| |||||||||||||||||||| ||||| ||||||||||||||||  ||||| |||||||||||| ||||| |||||||||||  | |  || |  | || |   |  |   |  ||| | ||    | | | ||    ||    ||    | |   | ||    ||    ||   |  ||  
TTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattgtgtgtgtgtgtgtgtttatacatatatgctttac---tttttggttcttttcatgcatttgacaagctttttgccttcctttatttgttatgt

upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G170148_T01 (Zea mays), 5'ss of exon 6
TTTTGCACAAGTATACAGCTTTCTGGGAAGCATATTTGATCCAGATACTAGTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttcttgagatttgagatatagtttctgaatgttctatgatt-----atatcgtatccttttcccaacacagatattcttaattttgaagtagcggaaat
|||||| | |||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||  ||||| | |||||||||||||||| || ||||||||  | | ||     |  |     |  ||||   |  | | |  ||       ||| |  |||||             ||     ||||  | ||         
TTTTGCCCGAGTATACAGCTTCCTAGGAAGCATATTTGATCCTGATACAAGTGGGCATTTGCAGAGGTTAAAAGTGATGGATCCAATTGATATTCAAACGgtacatcttttatatatatatgctcaacttcttggttctttttatttcataagcatcttgccctttctttgtttgttgcatgtcccatttcaaggttttt-----
















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|218486576|gb|FG956240.1|FG956240
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|218500576|gb|FG960552.1|FG960552
EST:     AGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGATATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: AGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|38474825|gb|CF958958.1|CF958958
EST:     GCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|88688887|gb|CI732463.1|CI732463
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|27545921|gb|CA764047.2|CA764047
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|218489538|gb|FG952484.1|FG952484
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|218481447|gb|FG951027.1|FG951027
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCCATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|29637643|gb|CB642652.1|CB642652
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|33678202|gb|CF306441.1|CF306441
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATG
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATG
EST: gi|27577453|gb|CB000148.1|CB000148
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAAAG                         GTACTACTGCTGATGAGAAATCTGGCCATGAACTTAA
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAA
EST: gi|88689244|gb|CI732820.1|CI732820
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|55408531|gb|CV720907.1|CV720907
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|88689640|gb|CI733216.1|CI733216
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|88691348|gb|CI733931.1|CI733931
EST:     GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: GTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
EST: gi|218494859|gb|FG953214.1|FG953214
EST:     TGGGCATTTGCAGACTTTAAATGGCGATGGATCCAATTGATGTTGAAACG                         GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT
genomic: TGGGCATTTGCAGACTTTAAA-GGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTT

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: 62 (upstream exon), 41 (downstream exon)
Score: 2

TTTTGCACAAGTATACAGCTTTCTGGGAAGCATATTTGATCCAGATACTAGTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttct ... aaattgacagGTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGCACAAGTATACAGCTTTCTGGGAAGCATATTTGATCCAGATACTAGTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGATGTTGAAACGgtatgtttcttgagatttgagatatagtttctgaatgttctatgattatatcgtatccttttcccaacacagatattcttaattttgaagtagcggaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA