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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggtaaaatttttgtag

Basic information

species Zea mays
transcript GRMZM2G164265_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatg----gattttttccttacataaatccattaaatggtaaaatttttgtag
 |||||||||||||| ||||||||||||||||||||||| || ||||||||| ||||||| ||||||||| ||   || ||||||||||||||||||||||||||     || | |   ||| | |||| ||     || |  |  | |||| ||| || |  |      |   | |||||
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatat-attttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtag

upper sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 3
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggtaaaatttttgtag-------------
||  |  || |||||||||||||| |||||||||||||| || ||||||||  |||||||   ||||||  |||   | || || ||||||||   ||||||     | |  || ||||| | ||    ||  |  ||||||    || | ||  || |    |   ||||     |             
CAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTGAAAGAACGGGACCTGATGCGCTTGAGgt--actatt--caaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacag
















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|78113587|gb|DV531978.1|DV531978
EST:     GTCGAGGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCCATCGAA-CAGTAAAGGATG
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGC-ATCGAAACAGTAAAGGATG
EST: gi|67020152|gb|CO448901.1|CO448901
EST:     GGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|148950416|gb|EC895983.2|EC895983
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|28909993|gb|CB331203.1|CB331203
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|18654924|gb|BM499729.1|BM499729
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAANCAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|18661950|gb|BM501665.1|BM501665
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|149102516|gb|EE188222.2|EE188222
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|148937187|gb|EC881368.2|EC881368
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|148950557|gb|EC896134.2|EC896134
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggtaaaatttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC