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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggtatttaactattcatatgacagtgaatttcttctgttctattttaacaattgtttctttccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT

Basic information

species Oryza sativa
transcript LOC_Os08g20270.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g20270.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G016827_T02 (Zea mays), 3'ss of exon 2
gtaagttggtattta----actat-tcatatgacagtgaatttctt-----ctgttctattttaacaattgtttctttccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT
||||||||||||||     |  || |   |||   ||  ||| ||      ||||||| || | |||    || | |     |||||||| ||||| ||||||||||| || || ||||| |||||||||||||||||||| ||||||||||||||
gtaagttggtatttgttgtaggatgttggatgcatgttgattactaagctactgttctgttgtgacacgctttacctgtttctacagCCACGCTGGTTATTCATACTCGGGCCGATGTGCAGCTTATGCTTTTGGCAACATCGATCCAACTAACAT
















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|88369599|gb|CI582794.1|CI582794
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|88390884|gb|CI611110.1|CI611110
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|88826685|gb|CI777250.1|CI777250
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGGCGGTGTGCGGCTTATGCTTTTGGCA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGG-CGGTGTGCGGCTTATGCTTTTGGCA
EST: gi|88348987|gb|CI654031.1|CI654031
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|88288464|gb|CI661669.1|CI661669
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|40486364|gb|BX897928.1|BX897928
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGTTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|88371235|gb|CI597712.1|CI597712
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|66917040|gb|CX103888.1|CX103888
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|33810210|gb|CF330996.1|CF330996
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|58678103|gb|CK066790.1|CK066790
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
EST: gi|88417210|gb|CI576284.1|CI576284
EST:     AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCC                         CCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA
genomic: AGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAA

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), 69 (downstream exon)
Score: 34

CCAGGAAACTGGATGAGGAACTTGATGGTTGGCTGAGGGCTGCTGGTCTCACCAAGTCCCCTGATGTGAGGGCAGTAATTGCGCCgtaagttggt ... tccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgacagtgaatttcttctgttctattttaacaattgtttctttccattacagCCATGCTGGCTATTCATACTCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT
                           ttttaac  putative branch site (score: 34)
                                    ttgtttctttccatt  putative PPT
                         tattttaacaattgtt  TA-rich tract