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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgatcgttcgtgcccccttggctgaacacactggaactctgttcggtcacggagggaacaaagtccactaacacaactctacaatcctctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCAGGCAGAGACAGCTCTGAGCAGCATCCTTCCGTGTGTGGATGAGAGCACG

Basic information

species Zea mays
transcript GRMZM2G130868_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130868_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g03110.1 (Oryza sativa), 3'ss of exon 7
--atcgatcgttcgt-gcccccttggctgaacacactggaactctgttcggtcacggagggaacaaagtccactaaca-caactctacaatcctctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCAGGCAGAGACAGCTCTGAGCAGCATCCTTCCGTGTGTGGATGAGAGCACG
  | | | | ||  | |   || |  |  |||  | |     | | |  |||  |        ||  ||  | ||  | ||||  || |||| |   ||||||| |||||  |||||||||| |||||||||||  | ||||| || || ||||| |||||||||||||| |||| ||||||||| ||||| ||||| ||||| 
tgaaccagcattgatagtatccctcccaaaactaaatatgtttttatgaggttgcaatt----cactgtttagtattaacaacattataatctttctgcaacagTGCTGCAAAGGATACCTGTGAAGCAATGGATGAATGGGCACAACATCCTCAAGCAGAGACAGCTCTCAGCAACATCCTTCCATGTGTAGATGAAAGCACA
















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|16925628|gb|BM078696.1|BM078696
EST:     GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAG                         CGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
genomic: GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAGgtataacatt ... ctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
EST: gi|22490536|gb|BU050459.1|BU050459
EST:     GCTGTGGCGGCTCTCTTTATCCTTCTAGGCATTTTCCTGATACTAAACAG                         CGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
genomic: GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAGgtataacatt ... ctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
EST: gi|33100423|gb|CF060383.1|CF060383
EST:     GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAG                         CGCTGCGCAGGATACCTGCGAAGCAAAAGACCAGTGGGCCCAGCACCCTCA
genomic: GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAGgtataacatt ... ctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
EST: gi|87153175|gb|DY397964.1|DY397964
EST:     GCTGTGGCGGCTCTCTTTATCCTTCTAGGCATTTTCCTGATACTAAACAG                         CGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
genomic: GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAGgtataacatt ... ctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA
EST: gi|211182625|gb|FK950421.1|FK950421
EST:     GCTGTGGCGNCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAG                         CGCTGCGCAGGATACCTGCGAAS-AATGGACCAGTGGGCCCAGCACCCTCA
genomic: GCTGTGGCGGCTCTCTTTATCCTTCTAGGGATTTTCCTGATACTAAACAGgtataacatt ... ctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtcacggagggaacaaagtccactaacacaactctacaatcctctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCAGGCAGAGACAGCTCTGAGCAGCATCCTTCCGTGTGTGGATGAGAGCACG
                      cactaac  putative branch site (score: 1)
                                         tcctct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgatcgttcgtgcccccttggctgaacacactggaactctgttcggtcacggagggaacaaagtccactaacacaactctacaatcctctggcaacagCGCTGCGCAGGATACCTGCGAAGCAATGGACCAGTGGGCCCAGCACCCTCAGGCAGAGACAGCTCTGAGCAGCATCCTTCCGTGTGTGGATGAGAGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA