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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttggaaagatcctgccttcaagtcgtagctatttatcattacctgtattttattcattagaataccgatatgccttttttctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA

Basic information

species Zea mays
transcript GRMZM2G102898_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102898_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g05394.1 (Oryza sativa), 3'ss of exon 8
gtatgtttggaaagatcctgccttcaagtcgtagctatttatcattacctgtattttattcattagaataccgata--tgccttttttctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA
||||| | |  || ||  ||||||    || |  |||  |||    |    | |||     |  |    |  ||    |   ||| || | |||||||||||||| ||||| || || || || ||||||||||| || || ||||||||||||||||||| ||| || || || ||||||||||||||||||||||
gtatgct-gttaaaattatgccttt---tctttactacatatgtcgattcatctttaccaaagcaagcaattgaaggttttgtttcttgttatgcagGAATTATCAGAGCATCTTGGTATTCGTCTACTCAATGAAAGACTAAATGATCCTAACATGCAAGATTCTTTCGATTCGATCTTCCCAAAGGATCATCCGA

upper sequence: GRMZM2G102898_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g15420.1 (Oryza sativa), 3'ss of exon 7
gtatgtttggaaagatcctgccttcaagtcgtagctatttatcattacctgtattttattcat-tagaataccga--tatgccttttttctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA
||||||| |  ||  | |||| || |  |  ||      | |||  ||   | ||||||  |  ||||  |  ||  |||   ||| || | |||||||| || || || || || || || || |||||||| ||||  ||||||||||| |||||||||| ||| ||||| || || ||||||||||||||||| |
gtatgtt-gttaatgttctgcttttatttacta------tgtca--actcatcttttatcaaagtagacaattgaagtatatgtttattgttatgcagGAGTTGTCTGAACATCTTGGTATTCGTCTACTCAACGAGAAACTGAATGATCCCAACATGCAAGATTCATTTGATTCAATATTCCCAAAGGATCATCCAA
















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|22133466|gb|BQ833726.1|BQ833726
EST:     AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAA                         GAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
genomic: AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
EST: gi|26558338|gb|CA830573.1|CA830573
EST:     AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAA                         GAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
genomic: AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
EST: gi|87157479|gb|DY402268.1|DY402268
EST:     AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAA                         GAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
genomic: AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
EST: gi|211269527|gb|FL311774.1|FL311774
EST:     AGGAAGACACAACATCATCTTCTCGTATTTTCA-AAAAATATTGTTCCAA                         GAATTATCGGAGCACCTGGGCATACGC-TACTCAATGAGAGGCTGAATGAT
genomic: AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
EST: gi|60343026|gb|DN209999.1|DN209999
EST:     AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAA                         GAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT
genomic: AGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGAT

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

GGGGACTGATGCACTCCCTTGGCATGTTTTGGCTTACATCAGGTTGACAGAGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

GGGGACTGATGCACTCCCTTGGCATGTTTTGGCTTACATCAGGTTGACAGAGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GGGGACTGATGCACTCCCTTGGCATGTTTTGGCTTACATCAGGTTGACAGAGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GGGGACTGATGCACTCCCTTGGCATGTTTTGGCTTACATCAGGTTGACAGAGGAAGACACAACATCATCTTCTCGTATTTTCATAAAAATATTGTTCCAAgtatgtttgg ... tctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattacctgtattttattcattagaataccgatatgccttttttctgatgcagGAATTATCGGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTTGAGTCTATCTTCCCAAAGGATCATCCGA
                                            ttctgat  putative branch site (score: 116)
                                  tatgccttttttct  CT-rich tract
         tgtattttattcatta  TA-rich tract