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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAACTTGGTTAATTTGATTGGCTATTGTGCTGATGGAGACCAGCGACTTCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgctgttcttgtgtgttgtattgaatctgtttgcatatgaccatctggcagcattccaacccgtgtttctttgtgattaactgcatgcctgtt...

Basic information

species Zea mays
transcript GRMZM2G137468_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137468_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g30900.1 (Oryza sativa), 5'ss of exon 3
CAAAACTTGGTTAATTTGATTGGCTATTGTGCTGATGGAGACCAGCGACTTCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgctgttcttgtgtgttgtattgaatctgttt-gcatatgacc---atctggcagcattccaacccgtgtttctttgtgattaactgcatgcctgtt
|||||  | |||||| ||||||||||||||||||| ||||| || || ||||||||||||||||| |||| || ||||||| | |||||||||||||| ||||| ||| || |  || |    ||||  ||  |||||| ||||||||||   | |||  |   |||        |||||| |||   || |||||   |    
CAAAATCTTGTTAATCTGATTGGCTATTGTGCTGACGGAGATCAACGTCTTCTTGTTTATGAATACATGCACTTTGGATCATTGGAAGATCATTTGCATGgtacgaattctatgtttattccctgtagagatactgttttgcatatgaccacaacctgtaaattttctgttaatggtttctatgtctgtacctgcaatac----

upper sequence: GRMZM2G137468_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0146g00250.t01 (Vitis vinifera), 5'ss of exon 3
CAAAACTTGGTTAATTTGATTGGCTATTGTGCTGATGGAGACCAGCGACTTCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgctgttcttgtgtgttgtattgaatctgtt-tgcatatgaccatctggcagcattccaacccgtgtttctttgtgattaact--gcatgcctgtt----
|  ||| | || ||| |||| ||||| |||||||||||||| |||||||||||||| ||||||| |||||||   |||||||| || |||||  | |  ||||  |||    || |||  | |  |  ||  |||    | | ||  |  |||    | | ||     ||    |  || || |  | ||  |  | || |||    
CCTAACCTAGTGAATCTGATAGGCTACTGTGCTGATGGAGAACAGCGACTTCTTGTCTATGAATTTATGCCCCTGGGATCACTGGAGGATCACCTTCTTGgtaataat----tttttgcctataattctgtttctacgattcgtaaaataatca---atctttgtggacccaaataattggtaaaaagcttggtgttccagttttgg
















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|211477955|gb|FL115135.1|FL115135
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
EST: gi|26558503|gb|CA830738.1|CA830738
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
EST: gi|87156740|gb|DY401529.1|DY401529
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
EST: gi|22472491|gb|BU036971.1|BU036971
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAACTTGGTTAATTTGATTGGCTATTGTGCTGATGGAGACCAGCGACTTCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgctgttcttgtgtgttgtattgaatctgtttgcatatgaccatctggcagcattccaacccgtgtttctttgtgattaactgcatgcctgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA