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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

Basic information

species Zea mays
transcript GRMZM5G829894_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 4
---ttgtgacgaat-ggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
|| | | || | ||||||| ||||||| || || || || | || || | | || ||| || || | |||||| ||||| |||||||||||||||||||| || ||| |||||||||||||||||||||||||||| |||||||| || ||||||||||
ggtacatggcagttcaaattatctgaataacaggatttcatattagtattatttaacacatgtta---atcaatcataatatttctcctgtc-cacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
--ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttg--ttatgttttccccatctcggagctgc--agCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
|| | | | | | ||| ||| ||||| |||| | | || |||||| || | | || | || || || | ||| ||||| ||||| | ||||||||||| || || || |||||||| ||||| ||||| || ||||| ||||||||||||||||| |
gcatggcatgttcttgtgcatctactatgaggtagttgttttaacc---ttcc---tatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgtt---ccacttgtattcgatattttttg--ttatgttttccccatctcggag--ctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
| |||| | | | || || || | | | || |||||| || | | || | || || || || ||| ||||| ||||| | |||||||| ||||| || || |||||||| ||||| ||||| || ||||| |||||||||||||||||||
-------gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
ttgtgacgaatggataaactgaatatcaggattccaagcta-accacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
| | | | || | | ||| ||| | | | ||||| || || | || | ||||| ||| | ||| ||||| ||||| |||||||||| || ||||| || |||||||| | ||| ||||| || ||||| |||||||||||||||||||
tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttcc-ttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
------ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattt-tttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
|| | | | |||| | | | | | ||| || || || | | | || | |||| ||| |||| | | | ||| ||||| || || | |||||||| |||||||| | || ||| | |||||||||||||| ||||| || ||||| ||||||||||
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagt-cgctctgttt-tgtatggtactaatttgatat-ttttttttgttt----gtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG

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|60341056|gb|DN208029.1|DN208029
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
EST: gi|149099178|gb|EE185204.2|EE185204
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
EST: gi|166461242|gb|EG146934.1|EG146934
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAGG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGA
EST: gi|21481348|gb|BQ578031.1|BQ578031
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
EST: gi|33096324|gb|CF056318.1|CF056318
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA

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: 722

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGACCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 562

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGACCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 715

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGACCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 436

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGACCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
                                ttttccccatctcg  CT-rich tract
 atattttttgttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - aactgaa
- - - - - - - - - - - - - - - - -ccaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - cttgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtt