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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactttctcccttgtccttttcaggaactagtatatgtgtgaaatacctatctgttattcttgattgttgagtaaattatgacattttctgttctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G130749_T01 (Zea mays), 3'ss of exon 13
gtaaactttctcccttgtccttttcaggaactagtatatgtgtgaaatacctatctgttattcttgattgtt--gagtaaattatgacattttctgttc-------tttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG
             |   |   ||  | ||| |  | ||| |   || ||  ||| |  || ||  |    ||  ||| ||||||||| |  || ||||        |  | ||| ||||||| ||||||||||||| ||| |||||||||||||| ||||||||||| ||||| |||
-------------cagattacttggatgaagtgctctatata-aaattaaatatttcataatccagtccctttcgagaaaattatgatacattttgtttgcaattgtacaccagTTATGTGTTGCTGTTCCCTGCCACATACTCAAGTTCTGGGCTTTCTTAGGAATCATGCTTCAG
















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|29664361|gb|CB660636.1|CB660636
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29615462|gb|CB620474.1|CB620474
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29664325|gb|CB660600.1|CB660600
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|25803480|gb|CA759449.1|CA759449
EST:     GAAG-TGNCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTG-CTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29641508|gb|CB646515.1|CB646515
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29634262|gb|CB639271.1|CB639271
EST:     AGGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: AGGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29664362|gb|CB660637.1|CB660637
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29646484|gb|CB651491.1|CB651491
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|88520579|gb|CI448233.1|CI448233
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCCCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29614065|gb|CB619078.1|CB619078
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|66928227|gb|CX115075.1|CX115075
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
EST: gi|29615460|gb|CB620472.1|CB620472
EST:     GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG                         ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA
genomic: GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGA

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: 65 (upstream exon), 63 (downstream exon)
Score: 43

GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAGgtaaactttc ... tctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatctgttattcttgattgttgagtaaattatgacattttctgttctttatcagATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG
           tcttgat  putative branch site (score: 43)
                                     ttttctgttctttatc  putative PPT
                         taaattatgacatttt  TA-rich tract