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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcgactctgacacattgggtttgtgtgggaaactgtgtagtatccatgactaggtgaattcaaacacaaattggattctgcagtcaaaatata...

Basic information

species Zea mays
transcript GRMZM5G858197_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G858197_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g64730.1 (Oryza sativa), 5'ss of exon 2
GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactc---gactctgacacattgggtttgtgtgggaaactgtgtagtatccatgactaggtgaattcaaacac---aaattggattctgcagtcaaaatata
|| ||||| || ||||| || |||||||| ||||| |||||||||||||| ||| || |||| | |||||||||| | |||   ||| | ||||  |   || ||  ||    |   ||| | |  | ||| |  | | ||||          ||||| |   ||    ||   |   
GCCTATATTGCTGAGCTCGAGTCGCTGGTCACGCAACTCGAGGAGGAGAACGCCAAGATGTTCAAAGAACAGgtacttctccgagaccccgacatttctcgtgtgcttgtttga---tgttggaaacttgaatgtggggattcgtgtgttgagaattgaaccgtgtctccattgt---

upper sequence: GRMZM5G858197_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0055g00420.t01 (Vitis vinifera), 5'ss of exon 2
GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcgactctgacacattgggtttgtgtgggaaactgtgtagtatccatgactaggtgaattcaaacacaaattggattctg-cagtcaaaatata-------
||||| |  |  |||||||| |||||||| || ||||| ||||||||||||||   | | || |||||  ||||| |    |    |   |  ||  | | || ||  | | | |       | ||| || | |||||| | |    |  ||| ||||| |||   | || |        
GCTTACACAGTTGAGCTAGAGTCGCTGGTGACCCACCTGGAGGAGGAGAATGCACGGCTCTTAAGAGAGGAGgtattttgtgcaatttggat-ttaagatcgtatgctagatttta------ctatgcctggatgaatt-acatgggatatggcttctgacagattacatgtcgtgtggt
















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|211278317|gb|FL464695.1|FL464695
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|154130372|gb|EC872158.2|EC872158
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|211224501|gb|FL435966.1|FL435966
EST:     GCTGGTAACGGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAGG
genomic: GCTGGTAAC-GCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGA-G
EST: gi|37374163|gb|CF623418.1|CF623418
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|211132670|gb|FL468288.1|FL468288
EST:     CGCTGGTAACGCMCCTCGAGGAGGAGAATGCCSAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAARAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|149112568|gb|EE191364.2|EE191364
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|78544178|gb|DV621676.1|DV621676
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|37374161|gb|CF623417.1|CF623417
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|211278318|gb|FL464696.1|FL464696
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|32802198|gb|CD954434.1|CD954434
EST:     CGCTGGTAATGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAGGCGGCTTA
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTA
EST: gi|40303388|gb|CK347775.1|CK347775
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG
EST: gi|19769681|gb|BQ034402.1|BQ034402
EST:     CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG                         GAAGAGCGGCACCAGAAGCGGCTTAAAGAG
genomic: CGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcg ... tgtatttcagGAAGAGCGGCACCAGAAGCGGCTTAAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAGgtaatactcgactctgacacattgggtttgtgtgggaaactgtgtagtatccatgactaggtgaattcaaacacaaattggattctgcagtcaaaatata

- - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - GGAGAA