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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcctgtttgagataatgggataatgaaaagtgaatcatgcattgcttaattagaaactgggtattctgtttttcctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG

Basic information

species Zea mays
transcript GRMZM2G144254_T06
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144254_T06 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g31874.2 (Oryza sativa), 3'ss of exon 10
gtaggttcctgtttg-agataatgggataatgaaaagtgaatcatgcattgcttaattagaaactgggtattctgtttttcctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG
||  ||| ||||||| | ||| |    |||  |  ||  |||| ||  ||||| | | | |||||  |  || ||  || |||   | ||||||||||||| || |||||| | ||| |||||||||||||||||| ||||||| | || |||||||| || |||||||| |||| |||||
gtgagtttctgtttgtaaatattatcgtaagcatgag--aatcttgtgttgctca-tgataaactaagggttttggattgccttcattagGTATTTGATACCCTGAGGATAGTGATGTTTGTATTGGGCATGACATCTGTCTTTATAGGCATCTCCTTACTGGCACCCGACGACAGTAAAG
















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|60359035|gb|DN226008.1|DN226008
EST:     GTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|93281607|gb|EB673871.1|EB673871
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|32844477|gb|CD984158.1|CD984158
EST:     ACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: ACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|5296213|gb|AI782893.1|AI782893
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|6227147|gb|AW155676.1|AW155676
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|113701592|gb|EE679096.1|EE679096
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|211277446|gb|FL309933.1|FL309933
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|60350817|gb|DN217790.1|DN217790
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|60356320|gb|DN223293.1|DN223293
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|19822362|gb|BQ048386.1|BQ048386
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|32844487|gb|CD984168.1|CD984168
EST:     ACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: ACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|19822356|gb|BQ048380.1|BQ048380
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
EST: gi|78022546|gb|DV490933.1|DV490933
EST:     GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTC

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: 45 (upstream exon), 48 (downstream exon)
Score: 85

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 76

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 63

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 63

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcct ... cctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgaatcatgcattgcttaattagaaactgggtattctgtttttcctctgtcagGTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG
               gcttaat  putative branch site (score: 63)
                                   ttctgtttttcctctg  putative PPT
                 ttaattagaaa  TA-rich tract