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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctccctccctccttccatcccaccatgcaaaccgcttgatggcacctgacctttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT

Basic information

species Zea mays
transcript GRMZM2G335638_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335638_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g07960.3 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------------------gtatgttctccctccctccttcc----atcccac--------catgcaa--------------accgcttgatggcacctgacctttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT
                                                                             |||| |  |  || | |  | ||    | || |         || ||||              ||   || ||  || ||  | ||||  ||||| |||||||| ||||| |||||||||||| |||||||||||||  |||||||| || ||||| ||||||||||
gtaagatacctcattttcctctccttttcattttgcttattcttactcttcatgtgcacttgctcatgcacctgagagtatatcatatcttcattttccccaagacccgagagggttggcaggcaaggggtgaactgttaactcgttcataacatctagcatttgaccacagTGATATTTCATCCAATAACTTCAGTGGTTCATTACCACCTTCTCTGGGAAGCCTGTCATCATTGACTACATT
















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|16745940|gb|BM032370.1|BM032370
EST:     GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCT                         GGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
genomic: GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
EST: gi|18384547|gb|BM417746.1|BM417746
EST:     GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCT                         GGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
genomic: GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
EST: gi|16746060|gb|BM032490.1|BM032490
EST:     GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCT                         GGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
genomic: GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
EST: gi|18384548|gb|BM417747.1|BM417747
EST:     GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCT                         GGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
genomic: GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
EST: gi|18384557|gb|BM417756.1|BM417756
EST:     GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCT                         GGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
genomic: GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
EST: gi|18384652|gb|BM417851.1|BM417851
EST:     GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCT                         GGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG
genomic: GATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAG

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: 182

GTCACTGAATGATAACCATCTAGATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT


Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 54

GTCACTGAATGATAACCATCTAGATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 55

GTCACTGAATGATAACCATCTAGATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 137

GTCACTGAATGATAACCATCTAGATGGAAAGCTACCAGATGCATTTGATTCCCTCACGGGACTTGTAAATCTgtatgttctc ... ttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctccttccatcccaccatgcaaaccgcttgatggcacctgacctttgttcacagGGATATTTCTTCCAACAACTTCAGTGGTCCATTACCACCTTCATTGGGAAGCTTGACATCACTGACTACATT
                                    acctgac  putative branch site (score: 137)
                                          cctttgttc  CT-rich tract