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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattactttattgcacttgtgactgaaaaatccacctgtcctgtcctaacaaaaaaaagtaggaaacacattgttgataaacattttatccgcctaatggagcagtgccacaattgttgaacttgattgtgtctgactgtcttctggttattcaaaaatcaattaatcaattatctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA

Basic information

species Zea mays
transcript GRMZM2G018697_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 7
gtattactttattgcacttgtgactgaaaaatccacctgtcctgtcctaacaaaaaaaagtaggaaacacattgttgataaacattttatccgcctaatggagcagtgccacaat-tgttgaacttgattgtgtctgactgtcttctggtt-attcaaaaatcaattaatcaattatctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA
                                                                                    | | |      || |      || | || || || |  |    | | ||||| | |||  | || || | | |   || | |      |   |   || |||||||||||| | ||||| ||||| || ||||||||||| |||||  |||||||||||||||||||||| ||||||||||| |||||||| ||||||||||
----------------------------------------------------------------------------------tgtataacttatttattactattgttctactatatggtaga----aatatgtcttaatgttgtttgatttaattacttattattgttaggaactttaattgcagGTCCACATGCTAGATATTGAATGCTTCTCTTATCTTAATCGTGCTCTGGAGAGCCCATTATCACCAATTGTGATACTTGCGACAAATAGAGGAATATGTA

upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 7
gtattactttattgcacttgtgactgaaaaatccacctgtcctgtcctaacaaaaaaaagtaggaaacacattgttgataaacattttatccgcctaatggagcagtgccaca-attgttgaacttgattgtgtctgactgtcttctggttattcaaaaatcaattaatcaattatctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA
                                                                     | |||| |   |      ||    | |  |    |  | | | |   | |  | ||||||   || ||| |      | |||| |    |   | ||    |||         |||||||||||||| || || ||||| || ||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||| || || ||||||||||
---------------------------------------------------------------------ccttgtggggcagtgccatactgccatgctatttctctactatatggtataaatcttgatgtggtttgatt------tagttacttgtgaggaactt---taatcg-------cagGTCCACATGTTAGACATTGAATGCTTCTCTTATCTTAATCGTGCTTTGGAGAGCCCATTATCACCAATTGTGATACTTGCTACGAACAGAGGAATATGTA
















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|60340836|gb|DN207809.1|DN207809
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|22490622|gb|BU050545.1|BU050545
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|61118430|gb|DN559391.1|DN559391
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|113563309|gb|DW738296.1|DW738296
EST:     GGTGTTTTGTTCATTTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGA
genomic: GGTGTTTTGTTCA-TTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGA
EST: gi|87152471|gb|DY397260.1|DY397260
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|13126372|gb|BG316942.1|BG316942
EST:     CGATGAAGGAATTGCAGCAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTG
genomic: CGATGAAGGAATTGCAG-AGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTG
EST: gi|61118429|gb|DN559390.1|DN559390
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|31612366|gb|CD568988.1|CD568988
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|213174323|gb|FM191608.1|FM191608
EST:     TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTATTCATTGACGAG                         GTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAG

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: 174

GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 75

GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtattacttt ... tctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctgactgtcttctggttattcaaaaatcaattaatcaattatctttttcagGTCCACATGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTA
                                aattaat  putative branch site (score: 112)
                                          ttatctttttc  putative PPT
                   ttattcaaaaatcaat  TA-rich tract