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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcgatcaagagtctaaatctgaaacgggaaaattatatatacttgctacttggtcgcataacaacactatgtgacctggcaaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCT

Basic information

species Zea mays
transcript GRMZM5G879749_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g55130.5 (Oryza sativa), 3'ss of exon 7
-----gtaatcgatcaagagtc--taaatctgaaacgggaaaattatatatacttgctacttggtcgcataacaacactatgtgacctggcaaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCT
      |    || |  || |   | ||| |                ||  |  |  | |||    |   |  | |  | ||| || ||   ||| ||||| |||||||| ||||||||||| ||||| || || |||||||| ||  | || |||||||| |||||||  |||| ||||||||| || ||||||||||||
gtgagctggaggacctggaattggtgaatttatccttttggttcagcatggaactagttcttcagagatcatgagctatttgtcacttgatgaaaatgcagTGGCGACACGGATTCAGTCGTTCCGGTTACTGCAACGAGGTTTGCGCTTAGCCATCTTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCT
















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|93014933|gb|EB640453.1|EB640453
EST:     CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
EST: gi|76020008|gb|DT947178.1|DT947178
EST:     CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
EST: gi|71775052|gb|DR972930.1|DR972930
EST:     TGAAAGCAGGATTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: TGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
EST: gi|101395268|gb|EB819564.1|EB819564
EST:     CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
EST: gi|211058977|gb|FL460151.1|FL460151
EST:     CCGACGTACAAGAAGCTGATGAAAGCAGGACTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
EST: gi|91050417|gb|EB160835.1|EB160835
EST:     CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
EST: gi|211181832|gb|FL473669.1|FL473669
EST:     CCGACGTACAAGAAGCTGATGAAAGCAGGACTGAGGATATGGGTGTTCAG                         CGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG
genomic: CCGACGTACAAGAAGCTGATGAAAGCAGGATTGAGGATATGGGTGTTCAGgtaatcgatc ... aaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatacttgctacttggtcgcataacaacactatgtgacctggcaaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCT
                    gcataac  putative branch site (score: 3)
                      ataacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcgatcaagagtctaaatctgaaacgggaaaattatatatacttgctacttggtcgcataacaacactatgtgacctggcaaaactgcagCGGCGACACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT