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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATACTAAGATGCCTCGTGGATTTGGATTTGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatctaatttagatcgaccgtaacatgggaccttagcttccagctctgcaaacctctgcaatttagttgacagttagtttctctcgaaccctctcaacttcttgtttatgcag

Basic information

species Zea mays
transcript GRMZM2G139643_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139643_T05 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12850.1 (Oryza sativa), 5'ss of exon 4
GCATACTAAGATGCCTCGTGGATTTGGATTTGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatct-aatttagatcgaccgtaacatgggaccttagcttccagctctgcaaacctctgcaa--------tttagttgacagttagtttctctcgaaccctctcaacttcttgtttatgcag
|||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| ||||  |||||||||  |||| || |||||| | ||  | ||| |   ||  | | |||||        ||| | |     || | ||||||  | |   || ||||| || ||| | |||
GCATACTAAGATGCCTCGTGGATTTGGATTTGTTACATTTTCCGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAGCACGTTATAGATGGAAGAACGgtaggacatcttgatttagatcagccgttacgtgggacttcagtctacagttg-acactcttttgcaaagtcgcactttgggtttatcttggcttctctttatcttgcttaactt-ttatttgttcag

upper sequence: GRMZM2G139643_T05 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g02350.t01 (Vitis vinifera), 5'ss of exon 3
GCATACTAAGATGCCTCGTGGATTTGGATTTGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatctaatttagatcgaccgtaacatgggaccttagct-tccagctctg-caaacctctg-caatttagttgacagttagtttctctc-----gaaccctctcaacttcttgtttatg-cag
 |||||    | ||| || || ||||||||| | |||||| |||||||| ||||    || |||||||||||||| ||||| ||||||||||||||| | ||| | |  | || | ||  | |       |||  |  | || | | |  || || |  || | |  ||| ||  | | || || ||||| | |     ||      |    ||| |  || |  |||
ACATACCGGAAGGCCACGAGGCTTTGGATTTATAACATTTGCTGATCCAGCTGTGGCTGATAAGGTTTTGGAGGAAGATCATGTTATAGATGGCAGAGCAgtaagttgccaaactcagcccaat----gaatgatatttcagatgttcttctttgtctgacttttatcaacttgatgggca-ttggtttcaccctgttggagtttgttttgattcattcttgtatcag
















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|50336822|gb|CO531948.1|CO531948
EST:     CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
EST: gi|76014054|gb|DT941224.1|DT941224
EST:     CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
EST: gi|71417068|gb|DR803915.1|DR803915
EST:     CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
EST: gi|30088355|gb|CB886560.1|CB886560
EST:     CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
EST: gi|211508855|gb|FL158319.1|FL158319
EST:     CTGTTATAGACAAGGTTTTTGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTC
EST: gi|76282448|gb|DV022016.1|DV022016
EST:     CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
EST: gi|71768840|gb|DR966777.1|DR966777
EST:     CTGTTATAGACTAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
EST: gi|71446122|gb|DR827172.1|DR827172
EST:     CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACG                         GTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatc ... gtttatgcagGTTGAAGTTAAGAGGACTGTCCCGAGGGAAGAGATGATCACCAAAGACGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATACTAAGATGCCTCGTGGATTTGGATTTGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGATCACGTTATAGATGGCAGAACGgtaggatatctaatttagatcgaccgtaacatgggaccttagcttccagctctgcaaacctctgcaatttagttgacagttagtttctctcgaaccctctcaacttcttgtttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG