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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatacccctcatttcatgcttatttcagtgcttgggtctcactgtcctaatatatagGTTGTGTTAAAAGATGAAGTGGATGTTGATCCCAATGATCAGGCCTCTGTTCTTGAACATTTGGATAAAATT

Basic information

species Oryza sativa
transcript LOC_Os04g54340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g54340.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G106056_T02 (Zea mays), 3'ss of exon 11
gtatgatacccctcatttcatgctt---atttcagtgcttgggtctcactgtcctaatatatagGTTGTGTTAAAAGATGAAGTGGATGTTGATCCCAATGATCAGGCCTCTGTTCTTGAACATTTGGATAAAATT
| |||      |  | || ||||||   || | |||   |   ||||||  |    ||   ||||||||||| ||||||||||  |||||| |  | |||||||||| |||||| |||||||||||||||||||||
gcatgtcctttcgtacttaatgcttcgtatatgagttagtaaatctcacaattgatattcgtagGTTGTGTTGAAAGATGAAGCAGATGTTAACTCAAATGATCAGGACTCTGTGCTTGAACATTTGGATAAAATT
















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|29679603|gb|CB675878.1|CB675878
EST:     GGCCAACCAAAATACCTTTGAGATCCGTTAGGCCCTTTCACTATGCTGAG                         GTTGTGTTAAAAGATGAAGTGGATGTTGATCCCAATGATCAGGCCTCTGTT
genomic: GGCCAACCAAAATACCTTTGAGATCCGTTAGGCCCTTTCACTATGCTGAGgtatgatacc ... taatatatagGTTGTGTTAAAAGATGAAGTGGATGTTGATCCCAATGATCAGGCCTCTGTT
EST: gi|58585858|gb|CF984166.1|CF984166
EST:     GGCCAACCAAAATACCTTTGAGATCCGTTAGGCCCTTTCACTATGCTGAG                         GTTGTGTTAAAAGATGAAGTGGATGTTGCATCCCAATGATCAGGCCTCTGT
genomic: GGCCAACCAAAATACCTTTGAGATCCGTTAGGCCCTTTCACTATGCTGAGgtatgatacc ... taatatatagGTTGTGTTAAAAGATGAAGTGGATGTTG-ATCCCAATGATCAGGCCTCTGT

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: 63 (upstream exon), 31 (downstream exon)
Score: 4

GGAAACCAGTATAGGCCAACCAAAATACCTTTGAGATCCGTTAGGCCCTTTCACTATGCTGAGgtatgatacc ... taatatatagGTTGTGTTAAAAGATGAAGTGGATGTTGATCCCAATGATCAGGCCTCTGTTCTTGAACATTTGGATAAAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacccctcatttcatgcttatttcagtgcttgggtctcactgtcctaatatatagGTTGTGTTAAAAGATGAAGTGGATGTTGATCCCAATGATCAGGCCTCTGTTCTTGAACATTTGGATAAAATT
                                          tcctaat  putative branch site (score: 4)
                                       ctgtcct  CT-rich tract
                                             taatatata  TA-rich tract