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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgcaatgatacagccaatatgactgggattcttgtttcacattggtctgctgatgctaatatgatatagtagagtgcctttctgatatacaggctttggcattgtag

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 5'ss of exon 6
CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgcaatgatacagccaa--tatgactgggattcttgtttcacattggtctgctgatgctaatatgatatagtagagtgcctttctgatatacaggctttggcattgtag
||||| ||||| |||||| || |||||||||| ||||| |||||||| |||||||| || ||||||||||||     |   ||  ||| ||||  ||||  || | |   |||   | | | ||  ||| |  ||| ||  || |  |           ||||      || |||| || || ||
CTTCTTAATGTGAGCACAAATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAGgtaca---gtgctgccacaaccaaactatggttgag-tgactgtactaaactagtaggctaac-ctagtacaatttcat-----------ctgacgcttgggttttgacaatgcag
















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:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|74242073|gb|DT649987.1|DT649987
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAA                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTC
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTC
EST: gi|149095151|gb|EE180766.2|EE180766
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|148956344|gb|EC902151.2|EC902151
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|148938791|gb|EC883128.2|EC883128
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|78092275|gb|DV520649.1|DV520649
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|149009106|gb|EE041258.2|EE041258
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTACACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|148932140|gb|EC875563.2|EC875563
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|149071265|gb|EE159660.2|EE159660
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTT
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTT
EST: gi|71446471|gb|DR827521.1|DR827521
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|148972816|gb|EE023801.2|EE023801
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|149110343|gb|EE190365.2|EE190365
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAG                         GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA
genomic: ATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 412

CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 446

CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 334

CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 274

CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgc ... ggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTCAATGTAAGCACAGATAACATACTGATTCAGTCTACTGGTGTCATTGGTCAAAGGATAAAGAAGgtaggtacgcaatgatacagccaatatgactgggattcttgtttcacattggtctgctgatgctaatatgatatagtagagtgcctttctgatatacaggctttggcattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG