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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCGGGGACGACCCTAGCAAGTGGGACCCCGCCGAGTGCGACGCTCTCCTCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgcccttccaccgtttcttgggttgcttcactgaatcactgacggagattactagtatgaatttttgaaatgaacacagtgcttcataaaatt...

Basic information

species Zea mays
transcript GRMZM2G079452_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g23790.3 (Oryza sativa), 5'ss of exon 1
CCTCGGGGACGACCCTAGCAAGTGGGACCCCGCCGAGTGCGACGCTCTCCTCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgcccttccaccgtttcttgggttgcttcactgaa------tcactgacggagattactagtatgaatttttgaaatgaacacagtgcttcataaaatt
 || ||||||||||||  ||| |||||||| |||||||||||||| || ||||||||||| |||||||||||||||||||| ||||||||| ||| ||||||  || |    ||      |    |   ||  ||    ||         |||    ||||  | | | |     |   |     || |||| | ||         
ACTAGGGGACGACCCTTCCAAATGGGACCCGGCCGAGTGCGACGCCCTTCTCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggtttttttttcttttactgttatttatttggtagatggtcctctactatttgagagaaattggacattctgccgttgccaaaacagggtttggc------
















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|71311108|gb|DR791867.1|DR791867
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|76289326|gb|DV028894.1|DV028894
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|149112959|gb|EE295744.2|EE295744
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|211518581|gb|FL052087.1|FL052087
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCCGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|76012260|gb|DT939430.1|DT939430
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|71429968|gb|DR811018.1|DR811018
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|149107701|gb|EE189577.2|EE189577
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCACGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|71774790|gb|DR972668.1|DR972668
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|211518577|gb|FL052083.1|FL052083
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCCGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|211518580|gb|FL052086.1|FL052086
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCCGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|78090608|gb|DV518982.1|DV518982
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|211518579|gb|FL052085.1|FL052085
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCCGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|211518576|gb|FL052082.1|FL052082
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACWTGGAGATGGATGGTGCATTTGAGCCGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|211518582|gb|FL052088.1|FL052088
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCCGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|91051210|gb|EB161628.1|EB161628
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|149096864|gb|EE182658.2|EE182658
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|18963872|gb|BM660677.1|BM660677
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
EST: gi|71444932|gb|DR825982.1|DR825982
EST:     TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTG                         ATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG
genomic: TCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgc ... gtgtttgtagATGGAGGACATGGAGATGGATGGTGCATTTGAGCAGGTTGCTGTGGAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCGGGGACGACCCTAGCAAGTGGGACCCCGCCGAGTGCGACGCTCTCCTCCGCGGCGGGGAGCAGGTCGCCTCCGTGCTGCAGGAGATGGTCACGCTGgtcaggatgcccttccaccgtttcttgggttgcttcactgaatcactgacggagattactagtatgaatttttgaaatgaacacagtgcttcataaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatgaa