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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgactggccatgcatttcctttgcagtggcttccttgtgaatttgcttattctgacaatgtgtctgttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG

Basic information

species Zea mays
transcript GRMZM2G031107_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 15
---------gtttgtgactggccatgcatttcctttgcagt-ggcttccttgtgaatttgcttat-tctgacaatgtgtctgttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG
          | ||| | || |  ||  |  |  ||||| | ||||  ||||||| |      ||  |||||   ||||  |||    |||||| || ||||| |||||||||||  |||| ||||||||||| |  |||||| | | | || | |||||||||||||||||||| ||||| |  || ||||
gtttgtgctttgtgtaattgacgctgtgtgac--ttgcaatcggctcgcttgtgactgaatgaatacctgacgccgtgttggtt---ttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAGGTGAAGGCCCTGCCGTACAAGCCGGGAACCCGGGGACCCCCAGAGGCCG
















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|14203621|gb|BG837298.1|BG837298
EST:     GATAAGAGGAGACCAGCACGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCA-GCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|26456967|gb|CA828550.1|CA828550
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|6031397|gb|AW076299.1|AW076299
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCATGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|211247979|gb|FL192072.1|FL192072
EST:     ACGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCATGACATCGATGGTGGCAAG
genomic: ACGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|71596396|gb|DR907147.1|DR907147
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAC
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|78077421|gb|DV505855.1|DV505855
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|22521339|gb|BU080150.1|BU080150
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|78119963|gb|DV538347.1|DV538347
EST:     GATAAGAGGAGACCAGCAGCCCTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|45213774|gb|CK850005.1|CK850005
EST:     GATGAGCTGAGG                         GCCGCACTGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAA
genomic: GATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCA-TGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAA
EST: gi|88750685|gb|DY534826.1|DY534826
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|109179593|gb|EC380097.1|EC380097
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|51592845|gb|CV071991.1|CV071991
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|47962266|gb|CN844975.1|CN844975
EST:     GATAAGAGGAGACCAGCAGTACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|76281884|gb|DV021452.1|DV021452
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCTTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|78544145|gb|DV621643.1|DV621643
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|71595987|gb|DR906738.1|DR906738
EST:     TCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: TCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|22521338|gb|BU080149.1|BU080149
EST:     TTCGTTCGCCGAGATGAGCTGAGG                         GCCCCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: TTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|78109019|gb|DV527436.1|DV527436
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
EST: gi|62550472|gb|DN830892.1|DN830892
EST:     GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG                         GCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG
genomic: GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 68

GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 407

GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599

GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 163

GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGGgtttgtgact ... ttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtggcttccttgtgaatttgcttattctgacaatgtgtctgttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG
                            ttctgac  putative branch site (score: 163)
                tgaattt  TA-rich tract