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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcctgccttgctagtctccagagttctgaagttttgatagactgttcacatcagttgtgcttatattctctttgaaaaaaactgaattgcacagacagcaaaattttatatccattgtctcatctcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC

Basic information

species Zea mays
transcript GRMZM2G047894_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047894_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os03g18080.2 (Oryza sativa), 3'ss of exon 19
gtctgcctgccttgctagtctccagagttctgaagttttgatagactgttcacatcagttgtgcttatattctctttgaaaaaaactgaattgcacagacagcaaaattttatatccattgtctcatctcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC
                                               ||   | ||  | || ||| | ||| |||   ||    | | | ||    ||  |     ||||| ||   |  |||||||| | | |||||||||||||| || || ||||| ||| ||||||||||||||||||| || || |  ||||| ||||||||||||||||| |||||||| |||||||||||
-----------------------------------------------gtgtgcctcc-tcgtacttgttttcacttaagaagttcccgtagtgt---gatggattgtttttacatttgtgatctcatctaaccagcagTTGGACGGAATGCACAACACTTCATCACCTCCATTATCTGTGCGGGTTTGACGGCTGGAGTGGTAGCCTTGGTGAAAGCAAATGGGAAGCAGTTTTGCTC

upper sequence: GRMZM2G047894_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os03g18080.1 (Oryza sativa), 3'ss of exon 19
gtctgcctgccttgctagtctccagagttctgaagttttgatagactgttcacatcagttgtgcttatattctctttgaaaaaaactgaattgcacagacagcaaaattttatatccattgtctcatctcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC
                                               ||   | ||  | || ||| | ||| |||   ||    | | | ||    ||  |     ||||| ||   |  |||||||| | | |||||||||||||| || || ||||| ||| ||||||||||||||||||| || || |  ||||| ||||||||||||||||| |||||||| ||||||||   
-----------------------------------------------gtgtgcctcc-tcgtacttgttttcacttaagaagttcccgtagtgt---gatggattgtttttacatttgtgatctcatctaaccagCAGTTGGACGGAATGCACAACACTTCATCACCTCCATTATCTGTGCGGGTTTGACGGCTGGAGTGGTAGCCTTGGTGAAAGCAAATGGGAAGCAGTTTTG---
















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|78021557|gb|DV489944.1|DV489944
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|71428422|gb|DR809472.1|DR809472
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTTTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|78022411|gb|DV490798.1|DV490798
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|32934739|gb|CF039551.1|CF039551
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|37387638|gb|CF631017.1|CF631017
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|37391643|gb|CF633065.1|CF633065
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|31348859|gb|CD433216.1|CD433216
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|71325384|gb|DR799369.1|DR799369
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTTTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|18385140|gb|BM418339.1|BM418339
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|17970259|gb|BM277022.1|BM277022
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|24763373|gb|CA398549.1|CA398549
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|12968368|gb|BG265314.1|BG265314
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|113702249|gb|EE679753.1|EE679753
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
EST: gi|32850672|gb|CD990353.1|CD990353
EST:     AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG                         TTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA
genomic: AGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAA

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), 44 (downstream exon)
Score: 32

TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 56

TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 46

TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAGgtctgcctgc ... tcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgaattgcacagacagcaaaattttatatccattgtctcatctcatctgcagTTGGACGGAACGCGCAGCACTTGATCTCCTCCATTATCTGTGCGGGCTTAACAGTCGGAGTAGTAGCCTTGGTGAAAGCCAATGGGAAACAGTTTTGCTC
                                      tctcatctc  CT-rich tract
                    aaaattttatatccat  TA-rich tract