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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatcctacatgtatgttattgtaccaaatcagtatatttctattcctgacgtgagtcctctaaccccacccctttctgtggctttgtgcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGACGCAAGAACTTATGTCTGTGTCAGTGTGCGTTGATTATTTACGTGCGGTT

Basic information

species Zea mays
transcript GRMZM2G127141_T01
intron # 6
splice site 3'
intron type U2

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|19436217|gb|BM952627.1|BM952627
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GAT-ATTGAGGTTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCG
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGAT-GAG-TT-ATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCG
EST: gi|76010905|gb|DT938075.1|DT938075
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|149042023|gb|EE046997.2|EE046997
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|60356919|gb|DN223892.1|DN223892
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|78023551|gb|DV491938.1|DV491938
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|101387048|gb|EB815541.1|EB815541
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|211219872|gb|FL299417.1|FL299417
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|14883740|gb|BI273525.1|BI273525
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|74241511|gb|DT649425.1|DT649425
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|91876834|gb|EB406791.1|EB406791
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|14717616|gb|BI245266.1|BI245266
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTTTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|60399358|gb|DN232172.1|DN232172
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|71771177|gb|DR969114.1|DR969114
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|110223138|gb|EC905036.1|EC905036
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATTTGCTAGAGGCATATGAAGATCTTTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|88755737|gb|DY539878.1|DY539878
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTTTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|110494997|gb|EE014551.1|EE014551
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATTTGCTAGAGGCATATGAAGATCTTTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|76917704|gb|DV166966.1|DV166966
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|28986239|gb|CB351038.1|CB351038
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|60359685|gb|DN226658.1|DN226658
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|78091136|gb|DV519510.1|DV519510
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
EST: gi|17932520|gb|BM269480.1|BM269480
EST:     GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAG                         GATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC
genomic: GGAGGGAATCTTTAGCATTTAACCCAGAGCCTCCCTACTAATATCAAAAGgtctgtattc ... gcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgacgtgagtcctctaaccccacccctttctgtggctttgtgcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGACGCAAGAACTTATGTCTGTGTCAGTGTGCGTTGATTATTTACGTGCGGTT
               ctctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatcctacatgtatgttattgtaccaaatcagtatatttctattcctgacgtgagtcctctaaccccacccctttctgtggctttgtgcgagcgcagGATGATGAGTTATCTGCTAGAGGCATATGAAGATCTCTAGGTCCAGCGGACGCAAGAACTTATGTCTGTGTCAGTGTGCGTTGATTATTTACGTGCGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - -atgtatg
- - - - - - - - - - - tgtacca
- - - - - - - - - - - - - - - - - - - - - - attcctg