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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtataggaagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG

Basic information

species Zea mays
transcript GRMZM2G019358_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 14
gtatgtataggaagcacttcatcctgatattc-caattcacaatgtgctctttcttcccccaaaa-------------atgattttaacatt--cttcaaacatctt-------agGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG
||||||| ||| |||| ||  |  |    |||  ||    | | |   |  ||||||| ||| ||             || | ||| | ||    |||    || ||       ||||||||||||||||||||||| ||||    |||||||| |||||||||||||| ||| |||| || |  ||||| || |||
gtatgtagaggcagcatttgtttgttgccttcataagatgccacgccattcttcttcctccataagatcaaataaagcatcagtttcatataagtttcctgtattttttttttcagGGAAAGATATCAAGGGAAGAAATTGCTTTCATTTGTGTTGCAGCTCTGGCAAGTCCAAATGCAGTAGAGAAAACCTTTGAG
















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|78022714|gb|DV491101.1|DV491101
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|10450883|gb|BE924807.1|BE924807
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211357416|gb|FL471654.1|FL471654
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|7304470|gb|AW600409.1|AW600409
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|4730655|gb|AI649821.1|AI649821
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|13562283|gb|BG550503.1|BG550503
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|12968100|gb|BG265047.1|BG265047
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|32934374|gb|CF039186.1|CF039186
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGCCAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|7216720|gb|AW562842.1|AW562842
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG
                              ttttaac  putative branch site (score: 2)
                      aaaaatgattttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtataggaagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG