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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgctgttttaaagaatataatatgtacctcagtcctattgattgttattggttgcttccagcacagcaatttagatatactcccgcgggttct...

Basic information

species Zea mays
transcript GRMZM5G840928_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 5'ss of exon 4
ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc--------tgttttaaagaatataatatgtacctcagtcctattgattgttattggttgcttccagcacagcaatttagatatactcccgcgggttct
||||||||||||||  ||||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| | ||||||||||| || || |          | ||   || |||||    || ||| ||||| ||||        |||    | ||  |     ||||     |||    |||  || |
ATCTGTTTCTTCTAGAATTCTCACAGAAGTAGCAAAGTGGATGGAGCGCTTTGATTGCATCGTTGTTGGTCCTGGCCTTGGAAGGGACTCATTTCTTCTGgtcagcttacatacctaacatcttctggagtataaacactatctctgtcctgttga--------ggtcttcttcattagtcttatttgttgctacctttgcgttttat

upper sequence: GRMZM5G840928_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv05s0020g02800.t01 (Vitis vinifera), 5'ss of exon 4
ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgctgtt-ttaaagaatataatatgtacctcagtcct-----attgattgttattggttgcttccagcacagcaatttagatatactcccgcgggttct
| |  | ||    ||| |||| || || ||||  |||||||||||  | ||||||||| | || |||||||| ||||||||||||||||||||||| |||||  | ||  | |  |  ||   | |  |   ||  |    | |      |||| |  | |   |  ||     |  |  | || | || || |    |       
AGCAATCTCAGAGAAGGTTCTCACAGAGGTTGTTAAGTGGATGGAAAGATTTGATTGCCTAGTCGTTGGTCCAGGCCTTGGAAGGGACCCCTTTCTCCTGgtgtgcttcttttaatctaatgctttggtccctaaatttacctttgcaggttgaataatgtaattctctatttccttatgacttcaaat-tatttgtacac-----
















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|76282803|gb|DV022371.1|DV022371
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76011915|gb|DT939085.1|DT939085
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|71766337|gb|DR964274.1|DR964274
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|101395549|gb|EB819702.1|EB819702
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCCTGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|50330426|gb|CO525552.1|CO525552
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|89249729|gb|DY621515.1|DY621515
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76016158|gb|DT943328.1|DT943328
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|71448822|gb|DR829872.1|DR829872
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     TGATTGCATTGTTGTTGGTTCTGGCCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TGATTGCATTGTTGTTGGTCCTGG-CCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     TGGCCTTGGAAGGGACCCCTCTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     GCCTGGGAAGGGGACCCCTTTTTTCTG                         GAATGGGGGAGTAATATCATGAGGCACGCACGGCAGGCTAATATTCCAACT
genomic: GCCTTGGAA-GGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|89252939|gb|DY624725.1|DY624725
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|71767740|gb|DR965677.1|DR965677
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76018446|gb|DT945616.1|DT945616
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76282804|gb|DV022372.1|DV022372
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|78122651|gb|DV541035.1|DV541035
EST:     TGATTGCATTGTTGTTGGCCCTGGCCTT-GAAGGGGACCCCTTTCTTCTG                         GAGTGTGTGAGTAATATCATGAGGCACGCACGACGGGCTAATATTCCAACT
genomic: TGATTGCATTGTTGTTGGTCCTGGCCTTGGAA-GGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76912720|gb|DV164861.1|DV164861
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|211190743|gb|FL216452.1|FL216452
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCC-TTTCTTTTG                         GAATGTGTGAG
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAG
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgctgttttaaagaatataatatgtacctcagtcctattgattgttattggttgcttccagcacagcaatttagatatactcccgcgggttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcccgc