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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcccctcactcctcttcaatttcattaaattggtaaatactatggcttacatgtttgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTCAGTGTATTTGCCACCACCGAAACTTGATTTCACTTCTCAGCACCAGGAA

Basic information

species Oryza sativa
transcript LOC_Os08g34950.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 6
gtatcccctcactcctcttcaatttcattaaattggtaaatactatggcttacatgt--ttgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTCAGTGTATTTGCCACCACCGAAACTTGATTTCACTTCTCAGCACCAGGAA
|||     | |   ||  || || |  | | |||| |||    | |  |||||||||  ||  |||| ||||| |||||||||||||||||||||||||||||||| || |  || || || |||||||| |||||||| ||||||||||| |||||| |||| ||||||
gtacattattatctcttatccatcttgtcatattgttaagggttgtaccttacatgtgttttcatttcagCTTCGGTGAAATGGTTGCTTGCTTCCGATATGCATCAATTAGAGTCCACTCTGTGTATTTACCACCACCAAAACTTGATTTTACTTCTGAGCATCAGGAA
















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|33676698|gb|CF304937.1|CF304937
EST:     GTAGCCAGTTGTGGCCATTCTCTT-ACAGGGATTGCCTTCGTTTTTACGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
genomic: GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
EST: gi|33678298|gb|CF306537.1|CF306537
EST:     ATTCTCTTC-CAGGGATTGCCTTCGTTTTTACGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
genomic: ATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
EST: gi|33796202|gb|CF323967.1|CF323967
EST:     GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
genomic: GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
EST: gi|66915437|gb|CX102285.1|CX102285
EST:     GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTATGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
genomic: GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
EST: gi|33676578|gb|CF304817.1|CF304817
EST:     GTAGCCAGTTGTGGCCATTCTCTT-ACAGGGATTGCCTTCGTTTTTACGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATC
genomic: GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATC
EST: gi|569650|gb|D40499.1|D40499
EST:     GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
genomic: GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
EST: gi|88363129|gb|CI616286.1|CI616286
EST:     GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGG                         CTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC
genomic: GTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTC

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), 66 (downstream exon)
Score: 17

TTGGAAAATTTCTGGAACTTAGCTTCTCAAATCATGCGGCAGCTAGTAGGGTAGCCAGTTGTGGCCATTCTCTTCACAGGGATTGCCTTCGTTTTTACGGgtatcccctc ... tgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTCAGTGTATTTGCCACCACCGAAACTTGATTTCACTTCTCAGCACCAGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcttcaatttcattaaattggtaaatactatggcttacatgtttgtattttagCTTTGGTGAAATGGTTGCTTGCTTCCGATATGCATCGATCAAGGTTCATTCAGTGTATTTGCCACCACCGAAACTTGATTTCACTTCTCAGCACCAGGAA
                                 ggcttac  putative branch site (score: 17)
       aatttcattaaattgg  TA-rich tract