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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgcaactgcaactgcaatgcgcgggggctccggctgtgccgggcccaaaagagttggaattccgtgtgaaagctctgttcttgcgttggaatta...

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 1
GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagct-gcaactgcaactgcaatgcgcgggggctccggctgtgccgggcccaaaagagttggaattccgtgtgaaagctctgttcttgcgttggaatta
||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |||||||||||||||| |||||| |||||| |||||||||||||||||  || | ||     ||     ||||  ||   || || |   |    | |      |  |    | | || ||    |     | |   ||   |
GATGCTGGAGAGGATGAAGGATTACGGGCAGGAGGGCGCGTTCGCGCTCTGGGACGAGCTCTCGCCCGAGGACCGGGAGCTGCTCGTCAGGGACATCGAGgtgagcgagcgagtgagtgagctcaatgcggctgcgagggttgggagagagagagagagagagagagagagagagagagaga-gagagagagagagagaga
















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|149081508|gb|EE170644.2|EE170644
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211249747|gb|FL285802.1|FL285802
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|149015643|gb|EE045441.2|EE045441
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|40337292|gb|CK371362.1|CK371362
EST:     GGGACGATCTCTCGCCCGAGGACCGGGAGCTCCTCGTCCGGGACATCGAG                         AGTCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTT-GATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|149100896|gb|EE186991.2|EE186991
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211249750|gb|FL285805.1|FL285805
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|71429565|gb|DR810615.1|DR810615
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|148982619|gb|EE028417.2|EE028417
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211249751|gb|FL285806.1|FL285806
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211251970|gb|FL285809.1|FL285809
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|149090039|gb|EE179333.2|EE179333
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|78115803|gb|DV534191.1|DV534191
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|148956834|gb|EC902742.2|EC902742
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|91052249|gb|EB162667.1|EB162667
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|149014877|gb|EE044588.2|EE044588
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|148943648|gb|EC888712.2|EC888712
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211249749|gb|FL285804.1|FL285804
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|71757247|gb|DR955184.1|DR955184
EST:     GGGACGATCTCTCGCCCGAGGACCGGGAGCTCCTCGTCCGGGACATCGAG                         AGTCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211249748|gb|FL285803.1|FL285803
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGTGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|148990989|gb|EE032426.2|EE032426
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|94477177|gb|EB706135.1|EB706135
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|31354041|gb|CD438398.1|CD438398
EST:     GGGACGATCTCTCGCCCGAGGACCGGGAGCTCCTCGTCCGGGACATCGAG                         AGTCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|211249753|gb|FL285808.1|FL285808
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|76282035|gb|DV021603.1|DV021603
EST:     GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA
EST: gi|148966182|gb|EE017130.2|EE017130
EST:     GGGACGATCTCTCGCCCGAGGACCATGAGCTCCTCGTCCGGGACATCGAG                         AGCCTAGACCTCTCAGGGATCGATCGGATCATCCGGCGCTCCCTTGGATCG
genomic: GGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCA

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), 47 (downstream exon)
Score: 76

GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgca ... tgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTGGAGAGGATGAAGGACTACGGCCAGGAGGGCGCCTTCGCGCTCTGGGACGATCTCTCGCCCGAGGACCAGGAGCTCCTCGTCCGGGACATCGAGgtgagctgcaactgcaactgcaatgcgcgggggctccggctgtgccgggcccaaaagagttggaattccgtgtgaaagctctgttcttgcgttggaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC