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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggtgatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGG

Basic information

species Zea mays
transcript GRMZM2G069008_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069008_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggt-gatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGG
 ||     | ||   ||      | ||       |||        | | | | |  |   |     || |    || |  | | | | |   |  |  ||||| ||||| |||| ||||||||| ||||| | |||||| ||||||||||| || ||  | || |||||  |||||||    || ||  | || || ||  
attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggata-tatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT-
















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|149074765|gb|EE163195.2|EE163195
EST:     GGATGCTAGATGACGAANAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGGTATAA-GCTGAATATAGAAGACATGGTTGATCT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGG-TATAAAGCTGAATATAGAAGACATGGTTGATCT
EST: gi|71311098|gb|DR791863.1|DR791863
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|148991430|gb|EE032932.2|EE032932
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGAT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGAT
EST: gi|148942503|gb|EC887518.2|EC887518
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAAAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|67016855|gb|CO445604.1|CO445604
EST:     GGATGCTAGATGACGAAAAAGGTGATTCTGCTGGCACCGCAGTCCGTGAT                         GTGGAAGAAGAGACTGGTTTAAAGCTGAATATACAAAACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|76926121|gb|DV170728.1|DV170728
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgccactgataactgtatacattcttgtggcggtgatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGG
                 tatacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggtgatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG