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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaatcctcagcacatgagctctcttcttagtatacaggtcatggttatggtttatcgcagcatagtgtcagttctggagtctgaatggctgatggtctgttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG

Basic information

species Zea mays
transcript GRMZM2G022866_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022866_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g44400.1 (Oryza sativa), 3'ss of exon 9
gtctgaatcctcagcacatgagctctcttcttagtatacaggtcatggttatggtttatcgcagcatagtgtcagttctggagtctgaatggctgatggtctgttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG
                  |||   |||| | || |     | |     ||   ||||   |  || || || ||| ||  || |||||  ||   ||| | | |  ||  |||||||||| ||||||||| ||||||||||||| ||||| || || || || |||||  ||||||||||
---------------gtctgaatcctctgcatattgatacgtttgcatttgccgtttcctgtggcttactgccagatccagaatctgaccggtgcatgctttatcatc--agGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG
















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|14529382|gb|BI096515.1|BI096515
EST:     ACATTGCTTCAAAAGTCCCATCGCAGCCCATAGAGATATGGGCATATGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|211302326|gb|FL459923.1|FL459923
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|45847020|gb|CN070963.1|CN070963
EST:     ACATTGCTTCAAAAGTCCCATCGCAGCCCATAGAGATATGGGCATATGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|18167421|gb|BM337260.1|BM337260
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|78076799|gb|DV505233.1|DV505233
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|149086438|gb|EE175981.2|EE175981
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|12969746|gb|BG266636.1|BG266636
EST:     CATAGAGATATGGGCATATGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTG
genomic: CATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|71774726|gb|DR972604.1|DR972604
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA
EST: gi|5706290|gb|AI942066.1|AI942066
EST:     CATTGCTTCAAAAGTCCCTTCC-CAGCCCATAAAGATATGGGCATATGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTG
genomic: CATTGCTTCAAAAGTCCCA-CCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTA

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: 19 (upstream exon), 45 (downstream exon)
Score: 53

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG


Block sizes: 19 (upstream exon), 47 (downstream exon)
Score: 136

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG


Block sizes: 29 (upstream exon), 48 (downstream exon)
Score: 77

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG


Block sizes: 19 (upstream exon), 47 (downstream exon)
Score: 95

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcc ... gttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcagcatagtgtcagttctggagtctgaatggctgatggtctgttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG
                                 ggctgat  putative branch site (score: 95)
                                          tctgttttc  putative PPT