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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctgttactcttatattgctctatcagattgtttgtccttcttgggatactgatctgttcattcactagtcatttgccgcatgggcaaaatgaa...

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA19G37750.2 (Glycine max), 5'ss of exon 16
AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctgttactcttatattgctctatcagattgtttgtccttcttgggatactgatctgttcattcactagtcatttgccg-catgggcaaaatgaa
|||||| ||||||||||| ||||| |||||  |||||  |||||||||||| || ||  | ||||||||||||||||||||||||||||||||||| |||||| |      | |  |  | |||   | |||     ||    || | ||    | | |  |  | ||| ||     ||        |   ||   |  | 
AACAAACAGAAGGTGGCTGGAAAAATGTGTAGCTTATGCTGAAAGTCATGACCAGGCCTTGGTTGGTGACAAGACAATTGCATTCTGGTTGATGGACAAGgtatttatctcttcaat-gttttgtgttctcatccatttgaaactgcatgctgcaataaagttcttatttacagcatataaaaaaatacttgcttgactat

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA03G35020.1 (Glycine max), 5'ss of exon 16
AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctgttactcttatattgctctatcagattgtttgt--ccttcttgggatactgatctgttcattcactagtcatttgccgcatgggcaaaatgaa
|||||| ||||||||||| ||||| |||||  |||||  |||||||||||| || ||  | ||||||||||||||||||||||| ||||||||||| |||||  |      | |   | | |||   | |||     ||||   ||| | ||    | |||  |  | ||| ||     ||       |   ||   |  | 
AACAAACAGAAGGTGGCTGGAAAAATGTGTAGCTTATGCTGAAAGTCATGACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAGgtgtttatctct-ccaatgttttgtgttctcat-ccatttgaaacctgcatgctgcaatgaagttcttatttacagcatataaaaaagacttgcttgactat

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 16
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 5'ss of exon 16
AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtac---tagctgttactcttatattgctctatcagattgtttgtccttcttgggatactgatctgttcattcactagtcatttgccgcatgggcaaaatgaa
 || || |||||||||   || |||||| || |||||  ||||||||| |||||||||||||||||||| || |||||||| |||||||| ||||| ||||||    ||| |   || |   | |   |  | |  ||| ||     || |  |     ||   |||||     | ||                         
TACCAACAGAAGGTGGTCAGAGAAGTGTATCTCTTATGCTGAAAGTCACGATCAAGCTCTTGTTGGTGATAAAACAATTGCCTTCTGGTTAATGGACAAGgtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtg--ttgttcgggttccag-------------------------

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 16
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 5'ss of exon 16
AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagct--gttactcttatattgctctatcagattgtttgtccttcttgggatactgatctgttcattc-actagtcattt-gccgcatgggcaaaatgaa---------------------------
 || || || ||||||   ||||| ||||||   |||   || |||||||||||||| |||||||| ||||| || || || |||||| | ||||||||||||| |  |  ||| ||  || | |   | | |||| |   |  | |  |   |    ||| || ||   ||   | || |||  |    || |    | | ||                           
TACCAACAGGAGGTGGGGAGAAAAATGTGTCGTCTATGCAGAGAGTCATGATCAAGCCCTTGTTGGAGACAAAACGATAGCTTTCTGGCTAATGGATAAGgtaccattttggttgctgatagactcagcaaacagaataactaacatcttactgtctttgaactcttaggtctggttgtaattcagataaattgttcgactaaatcttatgttttttacttgattatatag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 16
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 5'ss of exon 16
AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctgttactcttatattgctctatcagattgtttgtccttcttggg-atactgatctgttcattcactagtcatttgc-cgcatgggcaaaatgaa-
 || |||||||||||| | ||||| |||||  |||||  |||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||| |||||  ||   |||  |  || ||      |  | |    |  ||  | ||| | |||     | |  |||  | ||  |||   |  |  |    || || || 
CACCAATAGAAGGTGGTTGGAAAAATGTGTTGCTTATGCTGAAAGTCATGACCAAGCTCTAGTTGGTGACAAAACCATTGCATTTTGGTTAATGGACAAGgttatacaagttcttacta-ataatataaggaaagatctcatctatattgtgcatatca--ccgaccatagaatatgcataaacatgtctcaaaaatatcaaa

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|67035192|gb|CO463725.1|CO463725
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAA                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|32934500|gb|CF039312.1|CF039312
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGTATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|32920624|gb|CF025436.1|CF025436
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|101386689|gb|EB815361.1|EB815361
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|60345781|gb|DN212754.1|DN212754
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|27753880|gb|BM378072.1|BM378072
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGCATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|32864974|gb|CF004656.1|CF004656
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|32930900|gb|CF035712.1|CF035712
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
EST: gi|32921787|gb|CF026599.1|CF026599
EST:     ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAG                         GATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT
genomic: ATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGAT

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), 49 (downstream exon)
Score: 471

AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 13

AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctg ... cttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAAGCTCTTGTTGGTGACAAGACAATTGCATTCTGGTTGATGGATAAGgtactagctgttactcttatattgctctatcagattgtttgtccttcttgggatactgatctgttcattcactagtcatttgccgcatgggcaaaatgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA