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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagatacatgattttgcttcttgaaatatttccaatgtctggttgtatgaacagccaagaaaaagctctcaaattggtggctacaactcacgaagagt...

Basic information

species Zea mays
transcript GRMZM2G068277_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068277_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g02690.1 (Oryza sativa), 5'ss of exon 11
GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagatacatg-attttgctt----cttgaaatatttccaatgtctggttgtatgaacagccaagaaaaagctctcaaattggtggctacaactcacgaagagt
||| ||||| ||||||||||| |||||||||||||||||||||| |||||||||| ||||||   || || |||    |||| ||| ||   ||| | ||||  |   | |    |    || | |    | |   |  ||  |  ||  |      
GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgatacacccatcttactttccccttgtaatcttcaaaatatttggtcattaaatccttaatagcaatggttattactcatttactgaatatctagt-----
















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|211432853|gb|FL453388.1|FL453388
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAADTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|60400409|gb|DN233216.1|DN233216
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|211359393|gb|FL440514.1|FL440514
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAANTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|71428336|gb|DR809386.1|DR809386
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|60401584|gb|DN234391.1|DN234391
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|71443220|gb|DR824270.1|DR824270
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|76281959|gb|DV021527.1|DV021527
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|78122195|gb|DV540579.1|DV540579
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|50331676|gb|CO526802.1|CO526802
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|110488821|gb|EE012728.1|EE012728
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|45568053|gb|CK985878.1|CK985878
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|148948940|gb|EC894359.2|EC894359
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|110504829|gb|EE017437.1|EE017437
EST:     AGTATTTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|60347346|gb|DN214319.1|DN214319
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|50324448|gb|CO519574.1|CO519574
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|211359065|gb|FL430712.1|FL430712
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAADTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|44900277|gb|CK826822.1|CK826822
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|5915607|gb|AW053248.1|AW053248
EST:     TTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: TTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|211478808|gb|FL379717.1|FL379717
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|74237081|gb|DT644995.1|DT644995
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagatacatgattttgcttcttgaaatatttccaatgtctggttgtatgaacagccaagaaaaagctctcaaattggtggctacaactcacgaagagt

- - - - - - - - - - - AAAGAA
- - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaaa