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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTTTCCTTTAATTCTCTTGCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaatgattgtttttctctcatagatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcag

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 7
GGATCTTTCCTTTAATTCTCTTGCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaa-atgattgtttttctctcata-----gatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcag
|||||| ||||||||||| ||| ||||||| ||||||||| | |||||   ||||||||||||||| ||| |||| ||   |||  | ||||  | |||||     || ||| ||  || || ||   ||| | ||| ||  | ||  ||||||||||
GGATCTGTCCTTTAATTCCCTTACTGGTGATCTACCACAAAGTTTCACTGGATTGTCAAGCCTGAAAAAAGTgtatgatgcatgccttttttattttcatatcttagacatgcctcattagaatgttttgcat-taacccattcctttttcttctcag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 7
GGATCTTTCCTTTAATTCTCTTGCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaa----------tgattgtttttctctcatagatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcag
|||||| ||||||||||||||| ||||||| ||||||||| | |||||   ||||||||||||||| | | |||| ||||           || ||  |||  |||| || | ||| ||  || || ||   |||   | | ||||| |   ||||||||||
GGATCTCTCCTTTAATTCTCTTACTGGTGATCTACCACAAAGTTTCACTGGATTGTCAAGCCTGAAAAGAATgtatgaaatgacgcatgcctgtttactttcatctcctacacatgcctcattagaatgttttgc--attaacccattccttttcttctcag
















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|3107717|gb|D43457.1|D43457
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATT                         ATATCTGCAGNACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|58652520|gb|CK041200.1|CK041200
EST:     GTCAAGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|44665230|gb|CR278664.1|CR278664
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|29644649|gb|CB649656.1|CB649656
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|29624948|gb|CB629959.1|CB629959
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|88386689|gb|CI682838.1|CI682838
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATAT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATAT
EST: gi|58661405|gb|CK050085.1|CK050085
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAG--A--                         A-AT-T----AACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|58658124|gb|CK046804.1|CK046804
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATGGTC-AGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
EST: gi|29681108|gb|CB677383.1|CB677383
EST:     GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATT                         ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT
genomic: GCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCT

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: 72 (upstream exon), 66 (downstream exon)
Score: 24

GGATCTTTCCTTTAATTCTCTTGCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaat ... ttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCTTTCCTTTAATTCTCTTGCTGGTGACCTACCACAAGGGTTCACATCATTGTCAAGCCTGAAGAAATTgtaagaaaatgattgtttttctctcatagatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA