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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggactagccttgagactggctcgctgtcctcttcatttgtctattgcttcctcgtaatgaagtgatgtgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCCAAGAAATCGAGGCGCGAGCTAGCTGCTATGGAGAAGGAGCTGGCAGCTG

Basic information

species Zea mays
transcript GRMZM2G017525_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
----gtaaggactagccttgagactggctcgctgtcctcttcatttgt--ctattgcttcctcgtaatgaagtgatg--tgctgta---cagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCCAAGAAATCGAGGCGCGAGCTAGCTGCTATGGAGAAGGAGCTGGCAGCTG
    |||   | | |  ||  ||         |    |  | |||  |   |||    |   |  | ||  |  |||  || | |    |||||| ||||||||||||||||||| ||||| ||||| |||||    || || |||||   |||  | ||  ||||| | |||||||||||| | || ||  
gttagtatttatttgtttttggatattaatcttagatttctaattgataattataatcttagctaactgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
gtaaggactagccttgagactggctcgctgtcct----cttcatttgtctattgcttcctcg--taat-gaagtgatg--tgctgta---cagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCCAAGAAATCGAGGCGCGAGCTAGCTGCTATGGAGAAGGAGCTGGCAGCTG
|| || | |    |||    ||| |     || |     |  | |||   |||     ||    |||| |  |  |||  || | |    |||||| ||||||||||||||||||| ||||| ||||| |||||    || || |||||   |||  | ||  ||||| | |||||||||||| | || ||  
gttagtattt-ttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
















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|12046320|gb|BF728459.1|BF728459
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|60396927|gb|DN229746.1|DN229746
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|37393909|gb|CF634221.1|CF634221
EST:     CGTGCCACGAAAAGGATCAGAACCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|211146570|gb|FL325019.1|FL325019
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|60347061|gb|DN214034.1|DN214034
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|9953958|gb|BE640541.1|BE640541
EST:     CGTGCCACGAAAAGGATCAGAGTCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|78179137|gb|DV549510.1|DV549510
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|76930458|gb|DV172393.1|DV172393
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
EST: gi|6918473|gb|AW400003.1|AW400003
EST:     CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAG                         ATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC
genomic: CGTGCCACGAAAAGGATCAGAGCCTGAAAGACAAGGACGACGCAGTTGAGgtaaggacta ... tgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtcctcttcatttgtctattgcttcctcgtaatgaagtgatgtgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCCAAGAAATCGAGGCGCGAGCTAGCTGCTATGGAGAAGGAGCTGGCAGCTG
         ttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggactagccttgagactggctcgctgtcctcttcatttgtctattgcttcctcgtaatgaagtgatgtgctgtacagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCCAAGAAATCGAGGCGCGAGCTAGCTGCTATGGAGAAGGAGCTGGCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG