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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCAAATCCAATAACCAAATatcctttcttatatttggctgggtaattctttgtttttcatgatacttgtcaaactttctatgtccttaacgaataatcacat

Basic information

species Zea mays
transcript GRMZM2G105192_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105192_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g01100.2 (Oryza sativa), 5'ss of exon 9
GTGGCAAATCCAATAACCAAATatcctt----tcttatatttggctgggtaattctttgtttttcatga--tacttgtcaaactttctatgtccttaacgaataat-cacat--------
||||||||||||||||||||||||||||      | | ||||   |    |  |||    |    |  |  ||      ||   || ||| ||  || | | |  | || ||        
GTGGCAAATCCAATAACCAAatatccttggtgcatcagatttctttaatgagatctaatatcaaaacaaattaacctagaatagttatatttctgtagctatttgtgcaaatgaaataca
















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|16926851|gb|BM079919.1|BM079919
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|16922011|gb|BM075387.1|BM075387
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|17929411|gb|BM266371.1|BM266371
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|110220376|gb|EC902274.1|EC902274
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|18162838|gb|BM332677.1|BM332677
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|29544356|gb|CB604736.1|CB604736
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCNCTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|17932564|gb|BM269524.1|BM269524
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|18173199|gb|BM348587.1|BM348587
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|113700925|gb|EE678429.1|EE678429
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|18166790|gb|BM336629.1|BM336629
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|71426677|gb|DR807727.1|DR807727
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTTGGAAGAGTTGCTTCCA
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTT-GGAAGAGTTGCTTCCA
EST: gi|71426676|gb|DR807726.1|DR807726
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|67019146|gb|CO447895.1|CO447895
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|110522223|gb|EE026407.1|EE026407
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|91876287|gb|EB406244.1|EB406244
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|76288379|gb|DV027947.1|DV027947
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
EST: gi|71446062|gb|DR827112.1|DR827112
EST:     ACGGTGGCAAATCCAATAACCAAAT                         ATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC
genomic: ACGGTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCAC

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: 39 (upstream exon), 47 (downstream exon)
Score: 73

GTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTGGT


Block sizes: 22 (upstream exon), 49 (downstream exon)
Score: 101

GTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTGGT


Block sizes: 22 (upstream exon), 49 (downstream exon)
Score: 191

GTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTGGT


Block sizes: 22 (upstream exon), 47 (downstream exon)
Score: 43

GTGGCAAATCCAATAACCAAATatcctttctt ... ataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTGGT