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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactgcaaccgctgatgttaagttcttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATG

Basic information

species Zea mays
transcript GRMZM2G702490_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G702490_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
--atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactg-caaccgctgatgttaagttctt-at----gtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATG
   | ||| ||||| | |  |||||| | | ||   ||||    | ||  ||||    ||||||||||| |  || | | ||||| ||  || || ||     || |||||||||| || | ||||||||| ||||||||||||||||  || ||||||||||||||||||||||| |||||||| ||||||||||||||||||||||
ttgtttcaatatctgataagatggcccacatta--gacttacagttgt--ctgt----cttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG

upper sequence: GRMZM2G702490_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv03s0063g00290.t01 (Vitis vinifera), 3'ss of exon 2
atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactgcaaccg--ctgatgtta-----agttcttatg--tacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATG
         |  ||    |     |    ||| || |  ||    ||  | ||    |||   ||   |     |   ||| | |||     | || |||||  || |||||||||||   ||  | ||||| ||| | |||||||| || || ||||| ||||| ||||||||||| ||||| ||  | |||||||||||||| ||||
---------ttgaatgaaaaaattttctttatcaattgattaaacttgttatatgctttgagataatttattgtctatctgcttttagttgtattttttatggttaaagCTTGCAGGCCATGAGCTATATGAAGAACCTTTACCATCTGCTGGGATAATCACTGGAATAGGACCTGTGCATGGGCGACTTTGTATGTTTGTGGCTAATG
















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|20301507|gb|BQ164450.1|BQ164450
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATA
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATA
EST: gi|71430321|gb|DR811371.1|DR811371
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATA
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATA
EST: gi|20506849|gb|BQ279371.1|BQ279371
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGAT
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGAT
EST: gi|91050683|gb|EB161101.1|EB161101
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATA
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgtacttcttgttctagactgcaaccgctgatgttaagttcttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATG
                             cgctgat  putative branch site (score: 4)
                                          ttcttat  putative PPT
                                  atgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactgcaaccgctgatgttaagttcttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - gagcatg
- - - - - - - - - - - - - - - - - -cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg