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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacataatatttcctatgtattaattttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctag

Basic information

species Zea mays
transcript GRMZM2G017086_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 5
GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacataatatttcctatgtattaattttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctag
| ||||||||||||||||||||| | ||||||||||| || ||||||||||| ||||| || |||||||||||||||||||||||||||||  |  | |||||  ||  || ||| | |     | | ||||||||           ||  ||  | |  ||||   ||| |||||||  ||
GACACAGTGCTGGTCTTTATAACTTGGGGAATACATGTTACATGAATTCCACTTTGCAGTGCCTGCATTCTGTTCCAGAGCTGAAGTCAGCTTTATTGAGgttccactgaaaattgctttgaagtaagttttgaagaaaggaatttcttcttggctaac-tcatatgttt-tacttgtgcag

upper sequence: GRMZM2G017086_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 5
GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacataatatttcctatgtattaattttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctag------
| || | |||||||||||  ||| | || || ||||| ||||||||||| ||||||||||| || |||||||| || ||| | ||||||||  ||   | ||  |   |  | |     |    || |  ||     |  |||     ||   | ||||   | |  | |  ||||   |||      
GGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTAAgta-agttttttctaagacacaatttgacattttgctgcatttgaagctgagatgtgatg--aataatattaactttcttagaatcag
















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|211522096|gb|FL426854.1|FL426854
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTG
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTG
EST: gi|32934266|gb|CF039078.1|CF039078
EST:     TTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: TTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211020022|gb|FL404266.1|FL404266
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAG
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAG
EST: gi|211542655|gb|FL412583.1|FL412583
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTTAG                         CTATTCAGATACTG
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTG
EST: gi|241994792|gb|GR421145.1|GR421145
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211144966|gb|FL424885.1|FL424885
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|78121540|gb|DV539924.1|DV539924
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211168209|gb|FL421347.1|FL421347
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGT
EST: gi|211408393|gb|FL407128.1|FL407128
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAG
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAG
EST: gi|211513751|gb|FL391725.1|FL391725
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTG-TAAGAGGTAATGGCATTGACCAAGCTTCTCATAATT
EST: gi|32932531|gb|CF037343.1|CF037343
EST:     CA-TGNCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: CATTG-CAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211059996|gb|FL387688.1|FL387688
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAAGTAATGGCATTGACCCAGCTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTT
EST: gi|211099805|gb|FL386855.1|FL386855
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGAATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGA-TACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATT
EST: gi|32863109|gb|CF002791.1|CF002791
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211106564|gb|FL394472.1|FL394472
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|32935100|gb|CF039912.1|CF039912
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|32930082|gb|CF034894.1|CF034894
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|32945380|gb|CF050199.1|CF050199
EST:     TTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: TTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|32911302|gb|CF016114.1|CF016114
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211219147|gb|FL370888.1|FL370888
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAATAGGTAATGGCATTGACCAAGCTTCTCAT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCAT
EST: gi|32932473|gb|CF037285.1|CF037285
EST:     AGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAACCTTCTCATAATTT
genomic: AGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211085323|gb|FL409653.1|FL409653
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211254374|gb|FL402662.1|FL402662
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAG
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAG
EST: gi|74240015|gb|DT647929.1|DT647929
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211141962|gb|FL418179.1|FL418179
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCANCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTC
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTC
EST: gi|32931528|gb|CF036340.1|CF036340
EST:     TGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: TGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|67017287|gb|CO446036.1|CO446036
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211536230|gb|FL396283.1|FL396283
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|33094903|gb|CF054897.1|CF054897
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211335073|gb|FL428116.1|FL428116
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGTTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|31998167|gb|CD661962.1|CD661962
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211459123|gb|FL410721.1|FL410721
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|50332356|gb|CO527482.1|CO527482
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 204

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 241

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 227

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacataatatttcctatgtattaattttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT