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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaatcctgcctctcatatgccttcaaatcgaaggacttcactgatcaatttgggctaatcactcgttaatttattgtccttgtgcaatactttgttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 3'ss of exon 3
gtaagcaaatcctgcctctcatatgccttcaaatcgaaggacttcactgatcaatttgggctaatcactcgttaatttattgtccttgtgcaatactttgttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
|||||  ||| || |||||||| |  | |             ||     |  || | |   |||| | || || |  |||| |   | | ||||   |||||    |||| ||| |||||||||||||||||||||||||||||||| ||||| 
gtaagttaattctacctctcatctcacct-------------tttgacaaataaatggaagtaataattcattgaggtattctatgttttcaatgtattgttttc-tagGCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACA
















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|71298836|gb|DR785405.1|DR785405
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|74242073|gb|DT649987.1|DT649987
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|149095151|gb|EE180766.2|EE180766
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|148956344|gb|EC902151.2|EC902151
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|148938791|gb|EC883128.2|EC883128
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|78092275|gb|DV520649.1|DV520649
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|149000193|gb|EE037335.2|EE037335
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCCAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACTG
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACTG
EST: gi|149009106|gb|EE041258.2|EE041258
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|148932140|gb|EC875563.2|EC875563
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|211453339|gb|FL002421.1|FL002421
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGG
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGG
EST: gi|28873422|gb|CB329414.1|CB329414
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|149071265|gb|EE159660.2|EE159660
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|71446471|gb|DR827521.1|DR827521
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|148930889|gb|EC873334.2|EC873334
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAANACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|148972816|gb|EE023801.2|EE023801
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|149110343|gb|EE190365.2|EE190365
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
EST: gi|20301290|gb|BQ164233.1|BQ164233
EST:     CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACTGGTGAT
genomic: CCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACTGGTGAT
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     TTTGTATTGC-AGCATGTCCTTAGTACATCGAAAACA                         GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
genomic: TTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT

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: 208

GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACAgtaagcaaat ... gttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggctaatcactcgttaatttattgtccttgtgcaatactttgttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT
                                         ctttgtt  CT-rich tract
                 ttaatttattgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaatcctgcctctcatatgccttcaaatcgaaggacttcactgatcaatttgggctaatcactcgttaatttattgtccttgtgcaatactttgttgcaatagGGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC