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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgcactgatttgactaatgttatcgcgacactatatcag

Basic information

species Zea mays
transcript GRMZM2G174170_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174170_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g20340.1 (Oryza sativa), 5'ss of exon 3
AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgca-ctgatttgactaatgttatcgcgacactat-atcag
| || || || || || |||||||| || ||||||||||||||||| |||||||||||||||||| | || |  || ||  |  ||           |  | | | |||| | |||||||| |  || |  |||||| ||  |  |||| || | |||
AACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAGgtgtgtacg-tatacttgaattctcgtt-----------ggcagattttttcatgtttctgcatccaatatatctaatgctactgaaacacaattaccag

upper sequence: GRMZM2G174170_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G04550.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgcactgatttgactaa--tgttatcgcgacactatatcag-----------------
| |||||||||| ||| || ||||| || || || |||||||||||||||||||||||||| |||   |    ||     |  | |||||               |||||||||   | |  | | ||   ||   |  ||  | || |   | |  |                 
ACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAGgtgagtacatttatcattctcttactctcatcctaaacttgcggctgctttcttatgattaccattaattatttagactaatagagtgatatgttttgtgtttcgattacatgacag
















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|91055824|gb|EB166242.1|EB166242
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|91055824|gb|EB166242.1|EB166242
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|91055824|gb|EB166242.1|EB166242
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71299488|gb|DR785755.1|DR785755
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71299488|gb|DR785755.1|DR785755
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71299488|gb|DR785755.1|DR785755
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|91875180|gb|EB405137.1|EB405137
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|91875180|gb|EB405137.1|EB405137
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|91875180|gb|EB405137.1|EB405137
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|149112681|gb|EE295513.2|EE295513
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|149112681|gb|EE295513.2|EE295513
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|149112681|gb|EE295513.2|EE295513
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78118997|gb|DV537381.1|DV537381
EST:     AGTCCTAGTCCATTGCATGTCTGGGAAAAGTA                       
genomic: AGTCCTAGTCCATTGCATGTCTGGG-AAA--Agtaggtgtgt ... actatatc
EST: gi|78118997|gb|DV537381.1|DV537381
EST:     AGTCCTAGTCCATTGCATGTCTGGGAAAAGTA                       
genomic: AGTCCTAGTCCATTGCATGTCTGGG-AAA--Agtaggtgtgt ... actatatc
EST: gi|211350512|gb|FL033069.1|FL033069
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|71314755|gb|DR794000.1|DR794000
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71314755|gb|DR794000.1|DR794000
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71314755|gb|DR794000.1|DR794000
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78107085|gb|DV525503.1|DV525503
EST:     TGTGAAG-GGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTA                       
genomic: TGTG-AGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGG-AAA--Agtaggtgtgt ... actatatc
EST: gi|78107085|gb|DV525503.1|DV525503
EST:     TGTGAAG-GGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTA                       
genomic: TGTG-AGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGG-AAA--Agtaggtgtgt ... actatatc
EST: gi|78111707|gb|DV530104.1|DV530104
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78111707|gb|DV530104.1|DV530104
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78111707|gb|DV530104.1|DV530104
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|211350508|gb|FL033065.1|FL033065
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|211350508|gb|FL033065.1|FL033065
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|211350508|gb|FL033065.1|FL033065
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78107086|gb|DV525504.1|DV525504
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78107086|gb|DV525504.1|DV525504
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|78107086|gb|DV525504.1|DV525504
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71301897|gb|DR787018.1|DR787018
EST:     ATGTGAGAGGGAGAAAGCACGAGTCTTAGTCCATTGCATGCCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71301897|gb|DR787018.1|DR787018
EST:     ATGTGAGAGGGAGAAAGCACGAGTCTTAGTCCATTGCATGCCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|71301897|gb|DR787018.1|DR787018
EST:     ATGTGAGAGGGAGAAAGCACGAGTCTTAGTCCATTGCATGCCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|211352915|gb|FL033076.1|FL033076
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|211352915|gb|FL033076.1|FL033076
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|211352915|gb|FL033076.1|FL033076
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAA                         G
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcag-
EST: gi|84969786|gb|DW468209.1|DW468209
EST:     GCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTA                       
genomic: GCACGAGTCCTAGTCCATTGCATGTCTGGG-AAA--Agtaggtgtgt ... actatatc
EST: gi|84969786|gb|DW468209.1|DW468209
EST:     GCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTA                       
genomic: GCACGAGTCCTAGTCCATTGCATGTCTGGG-AAA--Agtaggtgtgt ... actatatc
EST: gi|211350511|gb|FL033068.1|FL033068
EST:     ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: ATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATTGGCACAATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 98

AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATTGGCACAATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATTGGCACAATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 71

AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgt ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATTGGCACAATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAgtaggtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgcactgatttgactaatgttatcgcgacactatatcag

- - - - GAGAGG
- - - - - -  GGAGAA