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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAACAGATGTTGATTGCTCTTCTAGGTGAATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtttggacatttgattaaaaaaatgtagttaaaatgtacgtaattctggtgtcttatgacagagttaagacttacaatgacttatgtggttaatggcag

Basic information

species Oryza sativa
transcript LOC_Os10g41510.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G015324_T02 (Zea mays), 5'ss of exon 6
GTAAAACAGATGTTGATTGCTCTTCTAGGTGAATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtt----tggacatttgattaaaaa---aatg---------tagttaaaatgtacgtaattctggtgtcttatgacagagttaagacttacaatgacttatgtggttaatggcag
             | |||||||||||||| ||||||||||||||  |||||||||| || |||||||||||||| || ||||||    |  ||||||  | | |||    |||         |  || |    ||  |  |||  ||| | |||    || ||||||||||||   | |||||||||  ||| |||
-------------TAATTGCTCTTCTAGGAGAATCAGAAATGAGGCTATCTGATGATATCATTGAGACAATCCTGGATAAGGTTCTTTTAAACATTTCTTCAGAAATCAGATGgttattgacttattgagtcataaattgttcctgtgacgtatactggaattaagacttacagcaagttatgtggt-gatgacag

upper sequence: LOC_Os10g41510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G107575_T01 (Zea mays), 5'ss of exon 6
GTAAAACAGATGTTGATTGCTCTTCTAGGTGAATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtt----tggacatttgattaaaaa---aatg--tagttaaaatgtacgtaattctggtgtcttatgac-agagttaagacttacaatgacttatgtggttaatggcag
|| || |||||||| |||||||| ||||| ||||||||||||||  ||||||||||||| |||||||||||||| || ||||||    |  |||||| || | |||   ||||  || || |    ||  |  |||  ||| | ||  ||  || ||||||||||||   | |||||||  | ||| |||
GTTAAGCAGATGTTAATTGCTCTCCTAGGAGAATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaaacatttcatcagaaatcaaatggttactttagtcataaattgttcctgtgacctaatactggaattaagacttacagcaagttatgtgaatgatgacag

upper sequence: LOC_Os10g41510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G015324_T06 (Zea mays), 5'ss of exon 3
GTAAAACAGATGTTGATTGCTCTTCTAGGTGAATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtt----tggacatttgattaaaaa---aatg---------tagttaaaatgtacgtaattctggtgtcttatgacagagttaagacttacaatgacttatgtggttaatggcag
|| || |||||||| |||||||||||||| ||||||||||||||  |||||||||| || |||||||||||||| || ||||||    |  ||||||  | | |||    |||         |  || |    ||  |  |||  ||| | |||    || ||||||||||||   | |||||||||  ||| |||
GTTAAGCAGATGTTAATTGCTCTTCTAGGAGAATCAGAAATGAGGCTATCTGATGATATCATTGAGACAATCCTGGATAAGgttcttttaaacatttcttcagaaatcagatggttattgacttattgagtcataaattgttcctgtgacgtatactggaattaagacttacagcaagttatgtggt-gatgacag

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|112785549|gb|EE590928.1|EE590928
EST:     AATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAG                         ACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAG
genomic: AATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtttggacat ... ttaatggcagACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAG
EST: gi|29657603|gb|CB653878.1|CB653878
EST:     AATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAG                         ACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAGCAGAG
genomic: AATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtttggacat ... ttaatggcagACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAG
EST: gi|89176813|gb|CI013386.1|CI013386
EST:     AATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAG                         ACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAG
genomic: AATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtttggacat ... ttaatggcagACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAG

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: 72 (upstream exon), 71 (downstream exon)
Score: 33

GTAAAACAGATGTTGATTGCTCTTCTAGGTGAATCAGAAATGAGATTATCTGATGAGATTATTGAGACAATCCTTGACAAGgtttggacat ... ttaatggcagACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAGTGGGAGAATTTTGTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTC




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