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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTAGTCCTCTCAGCGACGGCGCGAATGTCGCCAACTACACCGCTCTCATGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagtttttacgtacgtactcttcgttccatgcatataggtgtcgcacttcatgtggatagttagatagaacgaaatgcgatgctacaattaactgaag...

Basic information

species Zea mays
transcript GRMZM2G000842_T04
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000842_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g37170.3 (Oryza sativa), 5'ss of exon 10
CGCTAGTCCTCTCAGCGACGGCGCGAATGTCGCCAACTACACCGCTCTCATGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagtttttacg-tacgtactcttcgttccatgcatataggtgtcg-cacttcatgt-ggatagttag--atagaacgaaatgcgatgctacaattaactgaag
||   ||||||||| |||||||||  |||| |||||||||||||  ||||||||||| ||||||| |||||| || | ||||||||||||||| || ||||||||| ||| |  | | | ||  ||  | ||| | |   |    |  |  | | ||  ||||  |||   ||     ||||| |   |  | |||| ||||   
CGGCGGTCCTCTCAACGACGGCGCAGATGTTGCCAACTACACCGGCCTCATGGCCCTAGCACTTGGCAGGCTTGAGAACCTCGAGAGCTTTTATCGTCAGgtcagtatttcctcttcttcctagtccgtacatccttgctgtcaccatcgttgcttgcaggatgattaaccattttctgaaatacacag--aaaatttactg---
















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|88753493|gb|DY537634.1|DY537634
EST:     TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAG                         GCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
genomic: TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagttttt ... gcgaacgcagGCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
EST: gi|88758004|gb|DY542145.1|DY542145
EST:     TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAG                         GCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
genomic: TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagttttt ... gcgaacgcagGCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
EST: gi|78108046|gb|DV526464.1|DV526464
EST:     TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAG                         GCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
genomic: TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagttttt ... gcgaacgcagGCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
EST: gi|74246417|gb|DT654331.1|DT654331
EST:     TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAG                         GCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
genomic: TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagttttt ... gcgaacgcagGCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
EST: gi|91869978|gb|EB400638.1|EB400638
EST:     TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAG                         GCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
genomic: TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagttttt ... gcgaacgcagGCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
EST: gi|71760398|gb|DR958335.1|DR958335
EST:     TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAG                         GCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG
genomic: TGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagttttt ... gcgaacgcagGCGGACAGCCTGAGGCAGCAGACCTTGCACCAGATGCGGCGGATCCTGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTAGTCCTCTCAGCGACGGCGCGAATGTCGCCAACTACACCGCTCTCATGGCCCTGGCACTTGACAGGCTCGACACCCTCGAGAGCTTTTACCGCCAGgtcagtttttacgtacgtactcttcgttccatgcatataggtgtcgcacttcatgtggatagttagatagaacgaaatgcgatgctacaattaactgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT