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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaatgattgtttttctctcatagatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G153393_T01 (Zea mays), 3'ss of exon 7
gtaagaaa-atgattgtttttctctcata-----gatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT
||| ||   |||  | ||||  | |||||     || ||| ||  || || ||   ||| | ||| ||  | ||  |||||||||| ||| |||||||||| |||||||||||| ||||||||||| | || ||||||||||||||   | |
gtatgatgcatgccttttttattttcatatcttagacatgcctcattagaatgttttgcat-taacccattcctttttcttctcagGTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTT

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G330907_T01 (Zea mays), 3'ss of exon 7
----------gtaagaaaatgattgtttttctctcatagatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT
                   || ||  |||  |||| || | ||| ||  || || ||   |||   | | ||||| |   |||||||||| ||| |||||||||| |||||||||||||||||||||||| | || || || ||||||||    ||
gtatgaaatgacgcatgcctgtttactttcatctcctacacatgcctcattagaatgttttgc--attaacccattccttttcttctcagGTATTTGCAGAACAACCAATTTACTGGTTATATCAATGTCTTAGCCAACCTTCCCCTTGAAACCCT
















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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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagatatgtctttttggagtgacatgcctgtaatcccatactcgttcttctcagATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT
                                       tactcgttcttctc  CT-rich tract
         tcttttt  TA-rich tract