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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccacagaaacaattgttagctctcctaagagtagaatgcgcttattctaatttacactgtgatctaaatattttaggatataggaagttattttt...

Basic information

species Zea mays
transcript GRMZM5G866758_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os09g07830.3 (Oryza sativa), 5'ss of exon 10
TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccacagaaacaattgttagctctcctaagagtagaatgcgcttattctaatttacactgtgatctaaatattttaggatataggaagttattttt-
||| || ||||| |||||||| || ||||||||||||||||| ||||| ||||| || |||||  ||||| | |||||||| | ||| ||||||||||||||||||||||| | || || | | ||  | |||    | | ||  |    ||| |  |||  |   |     ||||  |  |  |  |||| | |   |  
TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccacagtatcacttctaatctgacttaaaca-atattgtacaccctctgaggtaccttaataaaatgatatggtttgtgaatggaaataagaatct

upper sequence: GRMZM5G866758_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 9
TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccacaga-------aacaattgttagctctcctaagagtagaatgcgcttattctaatttacactgtgatctaaatatt----ttaggatataggaagttattttt-----------------------------------
|||||| ||||||||| ||||||| ||||||||  ||||||| |   ||||||| ||||||||  ||||||  ||||  || ||||||||||| ||||| |||    | | |       || |     ||  ||| |  |   |||||       | |  ||    || | ||   |  | |||     |||  | |   | ||||||  |                                   
TGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAGgtacataaaatatattttaaatacgaactacatcttccgactatagaaaataagaaatagaaaaaccattttggcattcacattatttctagtgtttgatatgttattagtataatttcatactcatatgaggttgagctgtgcag
















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|17931054|gb|BM268014.1|BM268014
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|30088105|gb|CB886310.1|CB886310
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|101395308|gb|EB819584.1|EB819584
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|211193824|gb|FL472434.1|FL472434
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|31909501|gb|CD650950.1|CD650950
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|110525002|gb|EE029186.1|EE029186
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|93281704|gb|EB673968.1|EB673968
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|78087734|gb|DV516127.1|DV516127
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|76921549|gb|DV168617.1|DV168617
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|31909499|gb|CD650949.1|CD650949
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAGGCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|76284259|gb|DV023827.1|DV023827
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|30306466|gb|CD001139.1|CD001139
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|149016999|gb|EE154316.2|EE154316
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|76936635|gb|DV174816.1|DV174816
EST:     GGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: GGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|29544660|gb|CB605040.1|CB605040
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|32864390|gb|CF004072.1|CF004072
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|76017958|gb|DT945128.1|DT945128
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
EST: gi|32862142|gb|CF001824.1|CF001824
EST:     TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA                         GCCCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC
genomic: TTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATC

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), 47 (downstream exon)
Score: 115

TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 177

TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccaca ... gtttatacagGCTCCGGAGCTTTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAAgtaagccacagaaacaattgttagctctcctaagagtagaatgcgcttattctaatttacactgtgatctaaatattttaggatataggaagttattttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaacaa