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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctttcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcggtgctaaagctaaacagcta...

Basic information

species Zea mays
transcript GRMZM2G129155_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 5'ss of exon 17
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctt-tcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcggtgctaaagctaaacagcta
|||||||||||| || || ||||||||| ||||||||||||||||||| ||  |||||||||| ||||||||  | ||||| ||| | ||||||||  ||||  |||||   | ||  | | | ||  |   ||  |  | |   |   ||  | | |    ||| |   | |     |     |||| | |      |  
GCTTGAAATAGCAATAACTAAGTTGCTACTGAAGTCATATTACAATATAGTGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatcgttgtctcacttttctcattattactcgctttgcataggatggtgatttatttggcacattatttcgattataactaatgtttctggaca-

upper sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA15G06380.1 (Glycine max), 5'ss of exon 17
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctttcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcg---gtgctaaagctaaacagcta----
  |||||||| |  | ||||||||||| ||||  ||||| |||   |||||||| |||||||| |||||  | || || |||||| |||||||||||||||||     || |   |    | |||||   | ||        | |   | | | || |   | |||  |||| | ||||     || |  |   | | |  ||    
TATTGAAATAACAGTGACAAAGTTGCTTTTGAGATCATACTACGGCATTGTCAGAAAAAATGTTGAGGATCTTATCCCCAAAGCAATTATGCATTTCTTGgtac----tttactacttcatatccttgtagaattttcaaggtatataaatctaaaag---tagtaatcttttgctgtcttttatgttgcatacagaaaattagggt

upper sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA08G07160.1 (Glycine max), 5'ss of exon 17
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctttcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcggtgctaaagctaaacagcta---
  |||||||  |  | ||||||||||| ||||| ||||| ||  | ||||||||||||||||| |||||  |  | || |||||| ||||||| |||||||||  | ||     ||   | | | || |  ||     | |||    ||  |        ||| |     |||||        ||      ||    | |   
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttatattcttcttctaggctttgc--taaattgtttttcaattagatgccccaa-atgatgaatattagacaaataatctgctttcaatttccaaatt

upper sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA07G30150.1 (Glycine max), 5'ss of exon 17
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctttcggtatgcaatctttgt--gctatttttaatggc--atggtaggctttagatgtcggtgctaaagctaaacagcta
  |||||||  |  | ||||||||||| ||||| ||||| ||  | ||||||||||||||||| |||||  |  | || |||||| ||||||| |||||||||  |  |    |||   | | | || |   ||    | ||  |  | |  |   |||||   ||  ||| |  || | ||| |   | |   | || |    
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtacttcgtattcatcttctaggctttgcaaaatagttttttaattagatgctgcaaatggtgaatattagccaatataagtcagaagtcaccatcaaaa----

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|211024339|gb|FL478389.1|FL478389
EST:     AAAAGCAGTTATGCATTTCTTG                         GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
genomic: AAAAGCAGTTATGCATTTCTTGgtatgtgatt ... tctgttgcagGTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
EST: gi|32847928|gb|CD987609.1|CD987609
EST:     TCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAGTTATGCATTTCTTG                         GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
genomic: TCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgatt ... tctgttgcagGTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
EST: gi|88758145|gb|DY542286.1|DY542286
EST:     TCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTG                         GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
genomic: TCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgatt ... tctgttgcagGTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
EST: gi|37420874|gb|CF648134.1|CF648134
EST:     TCACGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTG                         GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT
genomic: TCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgatt ... tctgttgcagGTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctttcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcggtgctaaagctaaacagcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA