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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagtcttcttggacttctaactctcttttgaccctgtatagtcaggatccataatgttttgtgtttgcaacttgatctctaggagtttggctca...

Basic information

species Zea mays
transcript GRMZM2G044629_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 7
GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagtcttcttggacttctaactctctt----ttgaccctgtatagtcaggat-ccataatgttttgtgtttgcaacttgatctctaggagtttggctca
||||||||||||||||||||||| |||||||| |||||||| ||||| ||||||||||||||||||||||| | ||||| |   |||  ||    ||||||   ||      |||| | |||||    ||||    ||| ||   | |||   ||||||||| |    ||||||| | | 
GTGACATTTTTCCAACAAGGCACCCTTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAGgtaccatcttcta-ttatttttctaatcttccactgattgatcttgtattactaggaggtgatactgcggtttgta-acaacttgattttc--gagtttgacac-

upper sequence: GRMZM2G044629_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 7
GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtac---tacagtcttcttggacttctaactctcttttgaccctgtatagtcaggatccataatgttttgtgtttgcaacttgatctctaggagtttggctca---
|| || |||||||| ||||| ||| | || || |||||    ||||||||||||||||||||||| ||||| ||||||      || ||||    ||  | ||| | | ||||   | | | |  |  |  | | |||  || |||      ||    |  |  |  | |  || |     
GTTACCTTTTTCCAGCAAGGAACAATCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGGgtatactctcattctttactgagctgtaaatatatttt---cttctcttttttgctttcttaaatttatgtaaactaaa---aacatagaaaaatgagggtaccaa
















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|149015643|gb|EE045441.2|EE045441
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCT
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCT
EST: gi|40337292|gb|CK371362.1|CK371362
EST:     TTCCATGCGTTTCTGCCGATGGTAGTTTTATTATGGAGACAGCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
EST: gi|32941368|gb|CF046187.1|CF046187
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACAGCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
EST: gi|148982619|gb|EE028417.2|EE028417
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG                         GTAGCAAAGGCTCCTGATGGCA
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCA
EST: gi|149014877|gb|EE044588.2|EE044588
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG                         GTAGCAAAGGCTCCTGATGG
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGG
EST: gi|148943648|gb|EC888712.2|EC888712
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG                         GTAGCAAAGGCTCCTGATGGNCA-CGGTGGAGTTTATGCTG
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGG-CAACGGTGGAGTTTATGCTG
EST: gi|71757247|gb|DR955184.1|DR955184
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACAGCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGT
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGT
EST: gi|31354041|gb|CD438398.1|CD438398
EST:     TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACAGCATATAGG                         GTAGCAAAGGCTCCTGATGGCAACGGTGGA
genomic: TTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagt ... atgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGGgtactacagtcttcttggacttctaactctcttttgaccctgtatagtcaggatccataatgttttgtgtttgcaacttgatctctaggagtttggctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA