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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcacgggcccccggctctaaaaatcccactttcctctccctcctcttgccccagcctataagaaccaaaaattgcgaggaggggaaaatctgatctaaaaattccatcgattcattgagccaaagcagtactttgttcatgatgttgaaccttgttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC

Basic information

species Zea mays
transcript GRMZM2G158911_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158911_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g37060.1 (Oryza sativa), 3'ss of exon 1
gtaagctcacgggcccccg--gctctaaaaatcccactttcctctccctcctcttgccccagcctataagaaccaaaaattgcgaggaggggaaaatctgatctaaaaattccatcgattcattgagccaaagcagtactttgttcatgatgttgaaccttgttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC
|||| | |||    |||     |  |    |   |    |  | | || ||  || |   | || | |       |||  || ||  |    ||| |||||||  | | ||  ||   |  ||||    || |  ||  ||||||  || ||  |||             ||||| ||||||||||||  |||||| ||| ||||| | ||| |||||||||||||||||| ||| ||||| |||||||| ||| |||| |||||| |||||
gtaatcccaccactcccaaaaaccttggggagttcttgatttttttcccccaattccaagaacccagattgcttcaaatctgagattacttcaaa-tctgatccgagagttggat---tcgattggatgaatg--gttgtttgtttgtgttg--gaa-------------agGAATCTGCCGAGGCACCAGTTCGGGAACCTGCAGGGGAAGTTGTTCCCGGCCTACTTCATGCTCATCTCCGCCTGCGCCGCCGTCTCCGTCGCCGCCTTC
















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|211451131|gb|FL341690.1|FL341690
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211043407|gb|FL322270.1|FL322270
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211385514|gb|FL311825.1|FL311825
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211517546|gb|FL354935.1|FL354935
EST:     TGGGGCGCCGCC-TCTGGSCCACCTTTATCGGCGGSATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211406528|gb|FL321350.1|FL321350
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGNGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAAC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAAC
EST: gi|211467204|gb|FL319601.1|FL319601
EST:     TGGGGCGCCGCC-TCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGNATGTTCCCGG
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAG-ATGTTCCCGG
EST: gi|211212844|gb|FL308086.1|FL308086
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|149013529|gb|EE043016.2|EE043016
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211457504|gb|FL333177.1|FL333177
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAGGATGTTCCCGGG
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211401214|gb|FL312272.1|FL312272
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGN
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|15208758|gb|BI430642.1|BI430642
EST:     GGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTNCAA                         GAACCTGCCGGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCG
genomic: GGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTT-CAAgtaagctcac ... ttctttgtagGAACCTGCCG-AGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCG
EST: gi|211103781|gb|FL340542.1|FL340542
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211200603|gb|FL339165.1|FL339165
EST:     GGGGCGCCGCC-TCTTGGGC-ACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: GGGGCGCCGCCCTCT-GGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211008062|gb|FL363362.1|FL363362
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGMTGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211510286|gb|FL344839.1|FL344839
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211012242|gb|FL312906.1|FL312906
EST:     TGGGGCGCCGCC-TCTGGGSCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGTATGTTCCCGG
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAG-ATGTTCCCGG
EST: gi|211177136|gb|FL336664.1|FL336664
EST:     TGGGGCGCCGCC-TCTGGSC-ACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211442290|gb|FL322974.1|FL322974
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211208379|gb|FL341911.1|FL341911
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTTGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|32914143|gb|CF018955.1|CF018955
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|211322176|gb|FL319436.1|FL319436
EST:     TGGGGCGCCGCC-TCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
EST: gi|50334371|gb|CO529497.1|CO529497
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTT
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTT
EST: gi|211489054|gb|FL326662.1|FL326662
EST:     TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAA                         GAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC
genomic: TGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

GCGCCGTCACCGCTGCCAAGCTGGCCCACGTCCTCTCCTTTGCCACTTCCTGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

GCGCCGTCACCGCTGCCAAGCTGGCCCACGTCCTCTCCTTTGCCACTTCCTGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

GCGCCGTCACCGCTGCCAAGCTGGCCCACGTCCTCTCCTTTGCCACTTCCTGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 452

GCGCCGTCACCGCTGCCAAGCTGGCCCACGTCCTCTCCTTTGCCACTTCCTGGGGCGCCGCCCTCTGGGCCACCTTTATCGGCGGCATCATCATGTTCAAgtaagctcac ... ttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattgagccaaagcagtactttgttcatgatgttgaaccttgttctttgtagGAACCTGCCGAGGCACATGTTCGGCAACTTGCAGAGCAAGATGTTCCCGGCCTACTTCACGCTTATCTCTGCCTGCGCAGCCATCTCGGTCGCCACCTTC
                                        ccttgttcttt  CT-rich tract