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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttttttctcaatgtattccatttttgtttatgttgtatttgacaaatgttctatgatgtatttttacatgtgactagcatctgttgattagtt...

Basic information

species Oryza sativa
transcript LOC_Os08g29720.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G106703_T02 (Zea mays), 5'ss of exon 4
GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttttttctcaatgtattccatttttgtttatgttgtatttgacaaatgttctatgatgtatttttacatgtgactagcatctgttgattagtt-----
|| || ||  ||||| |||||||||| |||||||||||||| || ||||| ||||| ||||| |||| | |    || |  |||    |  |  |||| |||| |||   |||||||||||  ||   | || | ||     | ||||| || | ||| |     
GAGGGTTTCAGTAGACTATGGAGAGGAACAAATGCAGGCTTAGCATTAGCTGTACCCACTgtaagttatctgctacactccatttttgtggtcattatcttgttttt---aaatgttctatactgctctgttgcttgcag--aacatctatttagtagcttcaat

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G059018_T01 (Zea mays), 5'ss of exon 4
GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttttttctcaatgtattccatttttgtttatgttgtatttgacaaatgttctatgatgtatttttacatgtgactagcatctgttgattagtt---------
|| || || | |||| |||||||||| |||||||||||||| || ||||| ||||| ||||| |||| |||    ||      ||| |||||||     |||  |||    | ||||||||| ||   | |  | ||     | ||||| || | |||||         
GAGGGGTTCGTTAGACTATGGAGAGGAACAAATGCAGGCTTAGCATTAGCTGTACCCACTgtaagttctttgctaca------tccttttttgtggtcattgccttttttga-tgttctatgctgctctgtagcctgctg--aacatctatttaatagttttaatctgc
















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|218497482|gb|FG960434.1|FG960434
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|29661210|gb|CB657485.1|CB657485
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|58693531|gb|CK082218.1|CK082218
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|58672713|gb|CK061399.1|CK061399
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|25797756|gb|CA753717.1|CA753717
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|58607537|gb|CK035570.1|CK035570
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|7274031|gb|AU083575.1|AU083575
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAN-AGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|29680567|gb|CB676842.1|CB676842
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|218496315|gb|FG954193.1|FG954193
EST:     TGCAGG-TTGGCGTTAGCAGTACCAACT                         GTTGG-ATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: TGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
EST: gi|29677504|gb|CB673779.1|CB673779
EST:     GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT                         GTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT
genomic: GTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGAT

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: 60 (upstream exon), 73 (downstream exon)
Score: 46

GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttt ... ccataaacagGTTGGAATATATTTGCCTTGCTATGACCTATTTCGCAACTGGATTGAAGATTTTACACAAAGTAATGCTCCTGGTTTGACACCATATGCCCCATTAGTAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACTgtgagttttttttctcaatgtattccatttttgtttatgttgtatttgacaaatgttctatgatgtatttttacatgtgactagcatctgttgattagtt

- - - - - - - - - TGGAGA
- - - - - - - - - - GAGAGG