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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatttcacgcttgatattttaataacctgtggttaacagtatctgaatataagctgattcttactttatattggttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG

Basic information

species Oryza sativa
transcript LOC_Os02g14130.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 5
gtatgttcat--ttcacg-cttgatattttaataacctgtggttaacagt--atctgaatataagctgattcttactttatattggttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG
|||||| |||  || |    ||| | |   |||| | |   ||| | |||  ||||||||     |||||  | | || ||     |  | |||||| |||||  | ||||||||||| || ||||||||||||||||| || |||||||||
gtatgtccatattttataatttggtgtcacaatatctta--gttcatagttaatctgaat-----ctgatagtcagttcat-----tcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG

upper sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 5
gtatgttcatttcacgcttgatattttaataacctgtggttaacagtatctgaatataagctgattcttactttatattggttt-taatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG
|||||  |  | ||    | ||| |||  |  |      |    | | ||| ||| ||| |||| ||| |   |    |  ||  | |||||| ||||| || ||||||||||| || ||||||||||||||||| || |||||||||
gtatggcctgtccatatcttataatttggtttcacaaaatct-taat-tcttaat-taatctgaatctgatagtcagctcattcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG
















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|58685494|gb|CK074181.1|CK074181
EST:     ATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTG                         GTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAA
genomic: ATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTGgtatgttcat ... gttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAA
EST: gi|23514266|gb|BU673550.1|BU673550
EST:     ATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTG                         GTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAA
genomic: ATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTGgtatgttcat ... gttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAA
EST: gi|14981447|gb|BI306125.1|BI306125
EST:     ATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTG                         GTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAA
genomic: ATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTGgtatgttcat ... gttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAA

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: 51 (upstream exon), 67 (downstream exon)
Score: 21

ATATTCCGTGGTTTGGCTTACATTCATACTGTACCTGGAGTTTGCCACAGGGATGTGAAGCCTCAGAATCTTTTGgtatgttcat ... gttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggttaacagtatctgaatataagctgattcttactttatattggttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG
                             ttcttac  putative branch site (score: 21)
                                ttactttatattggtt  TA-rich tract