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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatatctccttacgacctcaaagccaaaccttgatgtagtcctatgttattacttttaaatcatgcaatgtccctgattattcattttcattctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTCATGGATCCGATGACCAGTGGGAATTTATTGGAGAGACAAGTACATCCAG

Basic information

species Zea mays
transcript GRMZM2G314386_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314386_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g49530.1 (Oryza sativa), 3'ss of exon 5
------ggatatctccttacgacctcaaagccaaaccttgatgtagtcctatgttattacttttaaatcatgcaatgt-ccctgattattcattttcattctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTCATGGATCCGATGACCAGTGGGAATTTATTGGAGAGACAAGTACATCCAG
        | |  | |||||  |     |||  ||| ||  ||| ||     ||| |     | ||||  |  |   | || | |  ||||  |||| ||   |||||||| ||||||||||||||||| || || ||||||||||| ||  |||| |||||||| ||||| || |||||||| ||||| ||| ||||||| || ||
aactcttaaaagatgcttac--ctattgagcagaacatt--tgttgtta---gttgtccaactaaaatggtctatcttgccttaaccattctgtttcctttctacagAATCTACAGATGATGAATCCAATTACGAATTTGAGTACGAAGTTCTGTCCCATGGATCTGATGAACAATGGGAATTCATTGGTGAGTCAAGTACGTCAAG
















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|60397446|gb|DN230262.1|DN230262
EST:     AATAACTGTCCCATCCTTGGTTGAAAAACAAG                         AATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTC
genomic: AATAACTGTCCCATCCTTGGTTGAAAAACAAGgtaattaagt ... attctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTC
EST: gi|76919523|gb|DV167760.1|DV167760
EST:     TGAAAAACAAG                         AATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTC
genomic: TGAAAAACAAGgtaattaagt ... attctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTC
EST: gi|149044644|gb|EE047616.2|EE047616
EST:     AACAGAATAACTGTCCCATCC-TGGTTGAAAAACAAG                         AATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTC
genomic: AACAGAATAACTGTCCCATCCTTGGTTGAAAAACAAGgtaattaagt ... attctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattacttttaaatcatgcaatgtccctgattattcattttcattctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTCATGGATCCGATGACCAGTGGGAATTTATTGGAGAGACAAGTACATCCAG
                           ccctgat  putative branch site (score: 4)
                                    ttcattttcattct  putative PPT
                                attattcattttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatatctccttacgacctcaaagccaaaccttgatgtagtcctatgttattacttttaaatcatgcaatgtccctgattattcattttcattctgacagAATCCACAGATGATGAATCCAACTATGATTTTGAGTACGAGGTCTTGTCTCATGGATCCGATGACCAGTGGGAATTTATTGGAGAGACAAGTACATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA