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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtttgttagttactctattgatggtgtggttagtctttatgtccatgcattttgttctgccaacatttataagaagagaactggaaacatataccactccctttttttttgcaattgctactgcagtgctaacctttgcctctattttcatatgcatcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG

Basic information

species Zea mays
transcript GRMZM2G047867_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047867_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g33710.2 (Oryza sativa), 3'ss of exon 10
gtgagtt---gtttgttagttactctattgatggtgtggttagtctttatgtccatgcattttgttctgccaacatttataagaagagaactggaaacatataccactccctttttttttgcaattgctactgcagtgctaacctttgcctctattttcatatgcatcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG
||    |   |||  ||| ||   | |||     | |  | ||   |||| ||  | | ||   |         || |||    |    | || ||  || | ||| ||   ||| || |  ||||| || | || || | | ||      ||   || ||| |  ||||  | ||     | |      |   || ||  |      | || | |  |    ||| ||||  |   |  |  |                               
gttcactaacgttatttaattctgccattctc--tttcataagctcttat-tctgtactttccctcaaatatgtatctattttcaccctaatgcaag-attt-ccattcaactttgttgtttaattgttagt-cattgatgaactg-----cttgcttaatagGT-TCAT--CGGG-----CTGCTTTTGTTC-TGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG----------------------------
















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|71333305|gb|DR803709.1|DR803709
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTTTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|18177971|gb|BM379181.1|BM379181
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|5871424|gb|AW017895.1|AW017895
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|60345911|gb|DN212884.1|DN212884
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|5740451|gb|AI948141.1|AI948141
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|37385273|gb|CF629769.1|CF629769
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTAGTACCTCTGCTGAAAAC                         GAGAAACCGAAAGAATCGGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|88757916|gb|DY542057.1|DY542057
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|93014144|gb|EB639664.1|EB639664
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGGTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|60350962|gb|DN217935.1|DN217935
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|88757915|gb|DY542056.1|DY542056
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTTTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
EST: gi|71757236|gb|DR955173.1|DR955173
EST:     TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC                         GAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA
genomic: TAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCA

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), 47 (downstream exon)
Score: 127

ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 114

ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 259

ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtt ... atcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattgctactgcagtgctaacctttgcctctattttcatatgcatcatgacagGAGAAACCGAAAGAATCAGTGTCAGAACCGCAGAAGATAAAGATATTGTCAAACAACGCCATTCTTACAGCTTCCTAGCCCTGAGCCGTACTCAATCTTG
                tgctaac  putative branch site (score: 259)
                                tattttcatat  TA-rich tract