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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttgcctcactgtatacctatgtttcatattttcagcaccctcgacactatcaacctgcacggacttgtgacctctttcttgattttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGATTAGTTGGGAAGTTTGAGGTGGCAGATGATATAACTCCAATCAAGATTG

Basic information

species Zea mays
transcript GRMZM2G120302_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 17
gttgttgcctcactgtat-acctatgtttc-atattttcagcaccctcgacactatcaacc-tgc-acggacttgtgac----ctctttcttgattttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGATTAGTTGGGAAGTTTGAGGTGGCAGATGATATAACTCCAATCAAGATTG
     | ||  ||||||| || | | | || ||| | |||   | ||  ||||  | |||| ||| |     ||||||          ||||   |||| |||||| |||||||||||||| || ||||||||||||||| ||||||||||  ||||||| ||||| ||| ||||||||||||||||||||||||||||||| |
----gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
















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|33091583|gb|CF051577.1|CF051577
EST:     TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
genomic: TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
EST: gi|5847476|gb|AW000555.1|AW000555
EST:     TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
genomic: TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
EST: gi|32935186|gb|CF039998.1|CF039998
EST:     TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
genomic: TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
EST: gi|32934798|gb|CF039610.1|CF039610
EST:     TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
genomic: TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
EST: gi|166434153|gb|EG144543.1|EG144543
EST:     CTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGGTGTTCTTTGCAAGA
genomic: CTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
EST: gi|148961815|gb|EE012596.2|EE012596
EST:     TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
genomic: TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
EST: gi|148972938|gb|EE023964.2|EE023964
EST:     TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAG                         GCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA
genomic: TGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCCGTAAGgttgttgcct ... ttttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctcgacactatcaacctgcacggacttgtgacctctttcttgattttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGATTAGTTGGGAAGTTTGAGGTGGCAGATGATATAACTCCAATCAAGATTG
                                       tcttgat  putative branch site (score: 4)
                                 cctctttcttgatttt  CT-rich tract
                                         ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttgcctcactgtatacctatgtttcatattttcagcaccctcgacactatcaacctgcacggacttgtgacctctttcttgattttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGATTAGTTGGGAAGTTTGAGGTGGCAGATGATATAACTCCAATCAAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG