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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgcttggaatgagctaggaggggttggagtttgggttccatatgtagttgcttggtgcttgggggttagttagggtggctatgaagttttgatgatgagaggggtattgatgtttgggttgcattcatggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCCAAGTCAATCGTTCTGTCTGGTGCGCTATCGGCGCTCTACGTGATGACG

Basic information

species Oryza sativa
transcript LOC_Os11g28300.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 3
gtacttgct--tggaatgagctaggaggggttggagtttgggttccatatgtagttgcttggtgcttgggggttagttagggtggctatgaagttttgatgatgagaggggtatt---gatgtttgggttgcattcatgg-tgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCCAAGTCAATCGTTCTGTCTGGTGCGCTATCGGCGCTCTACGTGATGACG
|||||   |  ||   ||||||||||||  |||   || ||        | |   | | || ||       |    ||    ||||| |||  ||| ||||    |  |  | ||   | ||||    ||   ||| | | ||||||||||||||||||| || || || ||||| ||||| ||||| |||||||||||||||||||| ||  |||||||||| ||||| ||||| || |||||||| 
gtactgattagtgatgtgagctaggaggatttgagtttcggaaatggcctctgtgtacctgctgtcctactgc--attgccttggctgtgagatttggatgtgtggctgtttcttcgagctgttcaattttttttctttgctgatgtagATTGGAGATGAGACATTCATCATTGCTGCGCTGATGGCGATGCGGCACCCCAAGTCAATTGTGTTGTCTGGTGCACTATCTGCGCTTTATGTGATGACA

upper sequence: LOC_Os11g28300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 3
gtacttgcttggaatgagctaggaggggttggagtttgggttccatatgtagttgcttggtgcttgggggttagttagggtggctatgaagttttgatgatgagaggggtattgatgtttgggttgcattcatggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCCAAGTCAATCGTTCTGTCTGGTGCGCTATCGGCGCTCTACGTGATGACG
                            ||  |||   |  || |  |||   ||  |||| || |   |||    ||  | | ||| |  |     ||||||  |   |||||||  | | |||               ||||||||||||||||| ||||| || || || || ||||||||| | ||||| || ||||| ||| | |||||||||||    ||  |    || ||||||
-------------------------ttattatagtg-agcctcaaactgttactg--tggtact-gtatgtttaccagttttgttat-atttgcatctgatgaatgttttattgataatggtgttat-------------tagATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG
















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|33804188|gb|CF327969.1|CF327969
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88569792|gb|CI660967.1|CI660967
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCC
EST: gi|88337293|gb|CI629583.1|CI629583
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTG
EST: gi|88307114|gb|CI640549.1|CI640549
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGC
EST: gi|88307842|gb|CI646277.1|CI646277
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCG
EST: gi|88380713|gb|CI634738.1|CI634738
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88426536|gb|CI579365.1|CI579365
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88349790|gb|CI634325.1|CI634325
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88353912|gb|CI634703.1|CI634703
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGG
EST: gi|88851485|gb|CI670925.1|CI670925
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88324987|gb|CI645001.1|CI645001
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGC
EST: gi|88403187|gb|CI570928.1|CI570928
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCG
EST: gi|88390701|gb|CI609326.1|CI609326
EST:     CCTGTTCGATGCGCTCTTCGCCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: C-TGTTCGATGCGCTCTTCGC-GAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88333978|gb|CI645392.1|CI645392
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAA
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAA
EST: gi|44678067|gb|CR291501.1|CR291501
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88415654|gb|CI591434.1|CI591434
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGGGCTAA
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAA
EST: gi|88401571|gb|CI588512.1|CI588512
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATT
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATT
EST: gi|88311914|gb|CI577520.1|CI577520
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88307697|gb|CI644736.1|CI644736
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTG
EST: gi|88335550|gb|CI642774.1|CI642774
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|218479784|gb|FG960708.1|FG960708
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88372059|gb|CI641694.1|CI641694
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATG
EST: gi|33677157|gb|CF305396.1|CF305396
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|66912648|gb|CX099496.1|CX099496
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|58589289|gb|CF987597.1|CF987597
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88348558|gb|CI634153.1|CI634153
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTA
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTA
EST: gi|88413071|gb|CI578922.1|CI578922
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGG
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGG
EST: gi|42592205|gb|CK738691.1|CK738691
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88400467|gb|CI593542.1|CI593542
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGGGCTAA
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAA
EST: gi|88422996|gb|CI615296.1|CI615296
EST:     GCTGTTCGATGCGCTCTTCGCGAGTCTCTCGAATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCG
genomic: GCTGTTCGATGCGCTCTTCGCGAGTCTCTCGA-TGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCG
EST: gi|87023908|gb|CI288261.1|CI288261
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88340660|gb|CI647464.1|CI647464
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGC
EST: gi|33687017|gb|CF315256.1|CF315256
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGTAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
EST: gi|88315632|gb|CI615504.1|CI615504
EST:     GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCT
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCT
EST: gi|88353597|gb|CI632988.1|CI632988
EST:     GGCTGTCCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAG                         ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC
genomic: GGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCC

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: 70 (upstream exon), 63 (downstream exon)
Score: 30

AGCAGTGGTGGAGGGAGACCATGGGGTGGCCCTCGATGAGGTCGGCCCCGGGCTGTTCGATGCGCTCTTCGCGAGTCTCTCGATGATCTTAGTCAGCGAGgtacttgctt ... ggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCCAAGTCAATCGTTCTGTCTGGTGCGCTATCGGCGCTCTACGTGATGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttttgatgatgagaggggtattgatgtttgggttgcattcatggtgatgtagATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCCAAGTCAATCGTTCTGTCTGGTGCGCTATCGGCGCTCTACGTGATGACG
                     tattgat  putative branch site (score: 30)
                     tattgat  TA-rich tract