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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCATGGATTTCTGATCCCTATAAAGACTGTGCTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgtatcatccttagcatatcatgcactactaataaactggtggttaaatggggatcttattagtaaacaaacatgtttgttgtggatccaaaac...

Basic information

species Zea mays
transcript GRMZM2G004459_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 8
CCCATGGATTTCTGATCCCTATAAAGACTGTGCTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgtatcatccttagcatatca-tgcactactaataaactggtggtta-aatggggatcttattagtaaacaaacatgtttgttgtggatccaaaac-------------------------------------------------
|||||||  |  | |||| |||   ||||||||||||| |||||| ||||||||  |||| |||||||| |||||||| |||||| ||| |  ||  || |||||     |   ||  ||| |   ||    ||  |  |       |||    ||  || |||| | |   |||    | |                                                   
CCCATGGTCTAATAATCCATATGTGGACTGTGCTGAAAGGAATGTCTTGGGTGGGTTGTCCCTTGAAGGATTTCTCTCCAAGgtagtctct--caaactaagcatgctgctatgctgataacactgtgtcaattgcagcgatagcactatctagaactaagcatgct-gcattggtgttagattttcttattatactatcttcctttgttgatgaactattctgcaattgcag

upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 8
CCCATGGATTTCTGATCCCTATAAAGACTGTGCTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgtatcatccttagcatatcatgcactactaataaactggtggttaaatggggatcttattagtaaacaaacatgtttgttgtggatccaaaac-----
 || |||  |||| |||  ||  |  ||||||||||||| ||||| ||||||||| ||||  ||||||| ||  |||| |||||||| | |  ||  ||| ||||   | |   |    | | |    | |  ||    | || || ||  | |   |      || | |   ||    |       
TCCGTGGTCTTCTCATCTGTACGAGAACTGTGCTGAAAATAATGTCTTGGGTGGTTTGTCGTTTGAAGGGTTCATCTCCAAGgtattttct--caaactttgcatgataagagttg---acacaacaattgacaaccctgtatttttttgttgatggattgaccttttagcaaattattatttgttg
















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|20512938|gb|BQ280124.1|BQ280124
EST:     CTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAG                         TGGGCTCTTATGACACTTCTAGATCCAACAAATAGTTATGCCAACCTTGCA
genomic: CTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgta ... tacgatgcagTGGGCTCTTATGACACTTCTAGATCCAACAAATAGTTATGCCAACCTTGCA
EST: gi|60340644|gb|DN207617.1|DN207617
EST:     CTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAG                         TGGGCTCTTATGACAC
genomic: CTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgta ... tacgatgcagTGGGCTCTTATGACAC
EST: gi|31358133|gb|CD442490.1|CD442490
EST:     CTGAAAT-AATGTGTTGGGTGGTCTGTCACTTGAAGGGTTTCTCTCAA-G                         TGGGCTCTTA-GACACTTCTAGATCCA-CAAATAGTTATGCCA-CCTTGCA
genomic: CTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgta ... tacgatgcagTGGGCTCTTATGACACTTCTAGATCCAACAAATAGTTATGCCAACCTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCATGGATTTCTGATCCCTATAAAGACTGTGCTGAAAAGAATGTGTTGGGTGGTCTGTCACTTGAAGGTTTTCTCTCAAAGgtattctgtatcatccttagcatatcatgcactactaataaactggtggttaaatggggatcttattagtaaacaaacatgtttgttgtggatccaaaac

- - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaca