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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctggagttcacttctatttttcctgttggaatagtttattttgtggcttctcttattttgattaacaatattgtgatctctttgttgtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGCTCTTGCTAGGCGTATTGCTAAAGTGGGGACTGCCTCCCGTCCTCTTCTA

Basic information

species Oryza sativa
transcript LOC_Os02g51410.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G161566_T03 (Zea mays), 3'ss of exon 4
gtatctggagttcacttctatttttcctgttggaatagtttattttgtggcttctcttattttgattaacaatattgtgatctctttgttgtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGCTCTTGCTAGGCGTATTGCTAAAGTGGGGACTGCCTCCCGTCCTCTTCTA
|||||| ||||||||| | |||| |    ||  ||| | |   |||||        || |||   | |||| |||||||| |   | |||  |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||||||||||| || || || ||||||||||| 
gtatctagagttcactcc-atttctttcttttaaatgggtcgctttgt-------tttctttgagtcaacagtattgtga-catgtcgttccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG

upper sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G070218_T01 (Zea mays), 3'ss of exon 6
gtatctggagttcacttctatttttcctgttggaatagtttattttgtggcttctcttattttgattaacaatattgtgatctctttgttgtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGCTCTTGCTAGGCGTATTGCTAAAGTGGGGACTGCCTCCCGTCCTCTTCTA
         |||     |||   || | |||      ||||       |   |  ||  | |  || || | |||||||| || || | || |||||||||| ||| ||||||| |||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||| 
---------gttggtacctagagtttcagttt-----gtttggacaaagaactgcctcttgtgaatcaatagtattgtgacctgtt-gatgcattatcagGAGATATATGAAGAGGGGCCTATCTGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGTATTGCTAAAGTGGGAACTGCCTCTCGTCCTCTTCTG
















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|218500073|gb|FG957690.1|FG957690
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCT
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCT
EST: gi|29687750|gb|CB684025.1|CB684025
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
EST: gi|29661027|gb|CB657302.1|CB657302
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
EST: gi|29660283|gb|CB656558.1|CB656558
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
EST: gi|58674778|gb|CK063465.1|CK063465
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
EST: gi|29660344|gb|CB656619.1|CB656619
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
EST: gi|29636670|gb|CB641679.1|CB641679
EST:     CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG                         GAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC
genomic: CGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGC

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: 70 (upstream exon), 74 (downstream exon)
Score: 25

AGTAGTGTCTTGAGGGATTTGTCCTCAATGAAGCGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTGgtatctggag ... gtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGCTCTTGCTAGGCGTATTGCTAAAGTGGGGACTGCCTCCCGTCCTCTTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggcttctcttattttgattaacaatattgtgatctctttgttgtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGCTCTTGCTAGGCGTATTGCTAAAGTGGGGACTGCCTCCCGTCCTCTTCTA
                  gattaac  putative branch site (score: 25)
         tcttattttgattaac  TA-rich tract