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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatctttacctatataaacatagtccacgtactgtcttgtttttttttatttttttgtctctcatcgtttcttttctgctgaaattcag

Basic information

species Zea mays
transcript GRMZM2G019986_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 13
GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatcttta------------cctatataaacatagtccacgtactgtcttgtttttttttatttttttgtctctcatcgtttcttttctgctgaaattcag
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GAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCCACAGCACTTTTTGAGgttcaacttctcagtcgcctatgctcttataacattctagatgtcatgctgtgtctttttgttatgattttgagaaactcatcggtatacatatctgaaaattcag
















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|149102321|gb|EE287688.2|EE287688
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|40303710|gb|CK348097.1|CK348097
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACGGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|78089271|gb|DV517645.1|DV517645
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|211406613|gb|FL094209.1|FL094209
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|16919474|gb|BM074209.1|BM074209
EST:     CCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGAAAAAATTCGCGCCGGTAAAGAACGCCAGCGGCGCGACA
genomic: CCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|5124174|gb|AI745798.1|AI745798
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACGGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|211288805|gb|FL433953.1|FL433953
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|211442520|gb|FL447109.1|FL447109
EST:     TTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: TTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18169117|gb|BM338957.1|BM338957
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18649167|gb|BM497986.1|BM497986
EST:     TTTATATTCGACGCCTTCACTTACTCCCCATCCACGGAGCCTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: TTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|16379775|gb|BI993142.1|BI993142
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18172348|gb|BM347736.1|BM347736
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|149111355|gb|EE294858.2|EE294858
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|110497708|gb|EE015394.1|EE015394
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|37387607|gb|CF631001.1|CF631001
EST:     AGTTNATATTCGACGCCTTCACTTACTCCCCATCCACGGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|110214878|gb|EC896775.1|EC896775
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|10450879|gb|BE924803.1|BE924803
EST:     AGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18164359|gb|BM334198.1|BM334198
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18166599|gb|BM336438.1|BM336438
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18166601|gb|BM336440.1|BM336440
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
EST: gi|18167755|gb|BM337595.1|BM337595
EST:     AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA
genomic: AGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACA

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), 48 (downstream exon)
Score: 96

GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACATACGACACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACATACGACACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACATACGACACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 475

GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatct ... tgaaattcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAACGGCGCGACATACGACACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCCACAGAGCTTTTCGAGgtcagaatctttacctatataaacatagtccacgtactgtcttgtttttttttatttttttgtctctcatcgtttcttttctgctgaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT