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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatctttggtgtgtcttgaatcgaagactactcatgttcttcttcttatgattctttgtggatatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG

Basic information

species Zea mays
transcript GRMZM2G077215_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077215_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g14950.1 (Oryza sativa), 3'ss of exon 4
---gtaatatctttggtgtgtcttg--aatcgaa--gactactcatgttcttcttcttatga----------------ttctttgtggatatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG
    |  ||| |||    |  ||||   |||  |  ||| |    | || |  || ||||||                || ||| |    ||||| ||||||||||||||||||||||| || |||||  |||||| ||  || ||||||| ||| |||| ||||||||| ||||||||||||
gtaatcctatgtttatcttaccttgcagatcacatcgaccataattcttgtggtttttatgaaagaaaaaaaatcttctttttttttttcatgttgaagGTAACTGGAGATCCTGGAAAAATTGTTGCTGTACAGAGGAACCTAAGCAAATTTGGAATCAAAGAAATTGCCAGAACTGGCAAG
















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|71424780|gb|DR806433.1|DR806433
EST:     TTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAG                         GTAACTGGAGATCCTGGNAAGATGGTTGCAATACAGAAGACTCTGAGCAAA
genomic: TTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAA
EST: gi|211008148|gb|FL252270.1|FL252270
EST:     AGACTACACACTAACTATTGRG                         GTAACTGGAGATCCTGGAAMGATGGTTGCAATACAGAAGACTCTGAGCAAA
genomic: AGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAA
EST: gi|67014257|gb|CO443006.1|CO443006
EST:     TTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTATACACTAACTATTGAG                         GTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAA
genomic: TTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAA

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: 63

ATAATGGGTTTGGTTCGCATTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 192

ATAATGGGTTTGGTTCGCATTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG


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

ATAATGGGTTTGGTTCGCATTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 115

ATAATGGGTTTGGTTCGCATTTTCAAAGCAGAAGTGGTTGATCTTTCAGACTACACACTAACTATTGAGgtaatatctt ... tatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcgaagactactcatgttcttcttcttatgattctttgtggatatgttaaagGTAACTGGAGATCCTGGAAAGATGGTTGCAATACAGAAGACTCTGAGCAAATATGGGATCAGAGAAATTGCTAGAACTGGCAAG
                                            atatgttaaa  TA-rich tract