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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgttattcatcaatcctgcattttctggctaccatgacgactggtgctgacctgatttactgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGATCATGGTCGATAGAAAATCCATCCAAAATGTTGGTCTTGCAGTGAGGTAC

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 19
---gtttgttgt--tattcatcaatcctgcattttctggctaccatgacgactggtgctgacctgattta---ctgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGATCATGGTCGATAGAAAATCCATCCAAAATGTTGGTCTTGCAGTGAGGTAC
    ||  ||||  ||||| ||  | |||||| | |    | ||||||| | || ||||||  || |||     ||||| ||||||||||||||||| ||||| ||||||||  |||||||||||||||| || ||||| || |||||||| || ||||| |||||| | || || ||  | 
gtttttccttgtagtattcttcc-ttctgcatatgccc-ttgccatgactagtgatgctgatttgtttttaatttgtggtagTGACATGGATTTGCATATGACCGCTCTTGCATTGGAACTTTGTTGCACAATAATGGTTGACAGAAAATCTATTCAAAACGTTGGTTTAGCTGTTAGAGAT
















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|88730915|gb|CI754528.1|CI754528
EST:     ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAG                         TGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
genomic: ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAGgtttgttgtt ... actgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
EST: gi|88347852|gb|CI635945.1|CI635945
EST:     ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAG                         TGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
genomic: ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAGgtttgttgtt ... actgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
EST: gi|88572034|gb|CI663605.1|CI663605
EST:     ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAG                         TGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
genomic: ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAGgtttgttgtt ... actgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
EST: gi|29634555|gb|CB639564.1|CB639564
EST:     ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAG                         TGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
genomic: ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAGgtttgttgtt ... actgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
EST: gi|88730224|gb|CI753839.1|CI753839
EST:     ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAG                         TGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT
genomic: ATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAGgtttgttgtt ... actgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGAT

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: 74 (upstream exon), 51 (downstream exon)
Score: 37

AGGCTACATTGGGAACACTAAATTCTCTTGTTGTTGCGTATGGTGGTCAAATTGGATCCTCTTATGAAACTATTATTGCTGAACTTTCTACGCTCATTAGgtttgttgtt ... actgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGATCATGGTCGATAGAAAATCCATCCAAAATGTTGGTCTTGCAGTGAGGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgcattttctggctaccatgacgactggtgctgacctgatttactgtggcagTGACATGGATTTGCACATGACTGCTCTTGCGCTGGAACTTTGTTGCACGATCATGGTCGATAGAAAATCCATCCAAAATGTTGGTCTTGCAGTGAGGTAC
      attttct  TA-rich tract