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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

Basic information

species Zea mays
transcript GRMZM2G022866_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022866_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
----tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG
       |||  |  | | |     |   |   ||  ||   |||     | |  ||   |||| |  || || |   | |  |||| | | | | |  ||||||||||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | |||||
tttcccttcacttaggatattt--gggtgttctttctgtctggaagaagtagt--gtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG

upper sequence: GRMZM2G022866_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatc--attcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG
||    ||| |      | |     |  |||      |   ||||| |   | |   ||  |    ||| |||  | | || ||  |        | |||||||||||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | |||||
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
















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|149104343|gb|EE289789.2|EE289789
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|18162906|gb|BM332745.1|BM332745
EST:     AATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: AATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|32940976|gb|CF045795.1|CF045795
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|60401026|gb|DN233833.1|DN233833
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|149026606|gb|EE046030.2|EE046030
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|76014575|gb|DT941745.1|DT941745
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|18171021|gb|BM340861.1|BM340861
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|78079812|gb|DV508224.1|DV508224
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|56462040|gb|CK986338.1|CK986338
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|71442261|gb|DR823311.1|DR823311
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|50324828|gb|CO519954.1|CO519954
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|134769080|gb|DY742751.1|DY742751
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|24934373|gb|CA452591.1|CA452591
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|71328184|gb|DR800730.1|DR800730
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATANAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|78079813|gb|DV508225.1|DV508225
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
EST: gi|50338487|gb|CO533613.1|CO533613
EST:     TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATG                         GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagac ... tctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG
                    tgttaac  putative branch site (score: 2)
                                           cctctatt  putative PPT
                             ttacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT