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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttgttttccttgatattgtgttacatttcccattaactggcatgctacagaccctgataagcttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGC

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 5
gtatgatttgttttccttgatattgtgttacatttcccattaactggcatgctacagaccctgataagcttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGC
||||| ||  || |  ||| | |||  ||   |||    ||     || ||  | | | | | || || |||  |||||||||| |||||||| ||||||||  | || ||||| || ||||| ||    || ||| || ||||||||||||||||||||||||| ||||| |||||||
gtatg-ttgattcttattggtcttgcattttcttttagcttctgcagc-tgtgagacatc-taattagtttccatttagGTTGCTGAGATCCTTAAGGATCGTGCATCGTGGTATCGCGATTGTCGGCATGTTGATGTCCTCCATGTTATCCCTACGGGTAACGGTGGAACGATTGAGC

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 4
gtatgatttgttttccttgatattgtgttacatttcccattaactggcatgctacagaccctgataagcttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGC
|| ||  |  || | |||| | |||   |   |||  | |   | |   ||| |||   ||| || |  |||  |||||||||| |||||||| ||||||||| | || ||||| || ||||| ||  | || |||||| ||||||||||||||||||||||||| ||||| |||||||
gtttg-ctgattcttcttggtcttgctgtttttttatcttctgcagctgtgcgaca---cctaattaatttccatttagGTTGCCGAGATCCTTAAGGATCGCGCATCGTGGTATCGCGATTGTCGGCGTGTTGATATCCTCCATGTTATCCCTACGGGTAACGGTGGAACGATTGAGC
















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|58656953|gb|CK045633.1|CK045633
EST:     GTGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG                         GTTGCGGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
genomic: GTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
EST: gi|58661675|gb|CK050355.1|CK050355
EST:     GTGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG                         GTTGCGGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
genomic: GTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
EST: gi|58654155|gb|CK042835.1|CK042835
EST:     GTGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG                         GTTGCGGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
genomic: GTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
EST: gi|58675209|gb|CK063896.1|CK063896
EST:     GTGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG                         GTTGCGGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
genomic: GTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
EST: gi|58675501|gb|CK064188.1|CK064188
EST:     GTGGCGTAGCAGCACGAGCTTGCGG-CTTGTGAGCCTTGAGCCCACAAAG                         GTTGCGGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
genomic: GTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGC
EST: gi|58609674|gb|CK037707.1|CK037707
EST:     GTGGCGTAGCAGCACGAGCTTGCGGGCTTGTGAGCCTTGAGCCCACAAAG                         GTTGCGGAGATCCT
genomic: GTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCT

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: 53 (upstream exon), 71 (downstream exon)
Score: 9

CCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAGgtatgatttg ... ttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttacatttcccattaactggcatgctacagaccctgataagcttcattttagGTTGCAGAGATCCTCAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGC
                                            cttcatttt  CT-rich tract
                                             ttcatttta  TA-rich tract