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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataggcatccaatatgtaatttgttctctggtgtctcttttgtatccggtttttttgtcccatacgctttttatttatgtttctgctaatctatttcagATATGGGTATACGGGAACAGCTTCGAATCTTCTCTCGTCGCCGTCGCCAACCCGAACCAGCAAGCTCTCGAGCGCTGGGCGGAACAGAACGGCGTCACCG

Basic information

species Zea mays
transcript GRMZM5G812228_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G812228_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ25426 (Selaginella moellendorffii), 3'ss of exon 16
gataggcatccaatatgtaatttgttctctggtgtctcttttgtatccggtttttttgtcccatacgctttttatttatgtttctgctaatctatttcagATATGGGTATACGGGAACAGCTTCGAATCTTCTCTCGTCGCCGTCGCCAACCCGAACCAGCAAGCTCTCGAGCGCTGGGCGGAACAGAACGGCGTCACCG
                                          ||     |   |     |    |   |    || |    | ||||   |    | ||||||||| |||| |||||||||||||||||||   | |||||||| |  | ||||||| ||  ||| |||||    |||||  |  | |||| |||||  |
------------------------------------------gttagttgccatgcgagcatcgagattgccaatattaactgctgccctttcgatccagATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATCCCGAACGAGGCAGCGCTCGATGCTTGGGCCAAGGAAAACGACGTCAAGG

upper sequence: GRMZM5G812228_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ23443 (Selaginella moellendorffii), 3'ss of exon 16
gataggcatccaatatgtaatttgttctctggtgtctcttttgtatccggtttttttgtcccatacgctttttatttatgtttctgctaatctatttcagATATGGGTATACGGGAACAGCTTCGAATCTTCTCTCGTCGCCGTCGCCAACCCGAACCAGCAAGCTCTCGAGCGCTGGGCGGAACAGAACGGCGTCACCG
                                          ||     |   |     |    |   |    || |    | ||| |  |    | ||||||||| |||| |||||||||||||||||||   | |||||||| |  | ||||||| ||  ||| |||||    |||||  |  | ||||  ||||  |
------------------------------------------gttagttgccatgcgagcatcgagattgccaatattaactgctgatctttcgatccagATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATCCCGAACGAGGCAGCGCTCGATGCTTGGGCCAAGGAAAACGATGTCAAGG
















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|110964187|gb|EE184087.1|EE184087
EST:     CAGTGGAAAATCTAGAGAATGTGTATGGTGTTCTTCAAGATATAGATTCG                         ATATGGGTATACGGGAACAGCTTCGAATTTTCTTTTGTCGCCGTCGCCAAC
genomic: CAGTGGAAAATCTAGAGAATGTGTATGGTGTTCTTCAAGATATAGATTCGgtatgtaaca ... tctatttcagATATGGGTATACGGGAACAGCTTCGAATCTTCTCTCGTCGCCGTCGCCAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccggtttttttgtcccatacgctttttatttatgtttctgctaatctatttcagATATGGGTATACGGGAACAGCTTCGAATCTTCTCTCGTCGCCGTCGCCAACCCGAACCAGCAAGCTCTCGAGCGCTGGGCGGAACAGAACGGCGTCACCG
                                       tgctaat  putative branch site (score: 2)
                                             tctatttc  CT-rich tract
                       tttttatttatgtttc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataggcatccaatatgtaatttgttctctggtgtctcttttgtatccggtttttttgtcccatacgctttttatttatgtttctgctaatctatttcagATATGGGTATACGGGAACAGCTTCGAATCTTCTCTCGTCGCCGTCGCCAACCCGAACCAGCAAGCTCTCGAGCGCTGGGCGGAACAGAACGGCGTCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT