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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcgtcgcatccttctttagacagaaatatcgctccctacccctgtctgattatctgcattcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA

Basic information

species Zea mays
transcript GRMZM2G052546_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g01750.5 (Oryza sativa), 3'ss of exon 4
-----------gtgctcgtcgcatccttctt----tagacagaaatatcgctccctacccctgtctgattatctgcattcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA
                  || || ||   ||     ||  | ||| | | || | || | ||||||||||| |||||||||||||||||| ||||||||||||||||| ||| || | |||||||| ||||| ||||||||| ||||||||||| |||| |||||
gttctcaaatatcatctatctcaaccaatttacagaaggaaaaaaaaacacttcttaactctgtctgattagctgcattcatgtgcagAGCCCACTTGATGTTGATAAACTTAGGGACATTGGTGTAAAAACAGTATTCTGCCTGCAGCAAGATCCAGACCTTGA

upper sequence: GRMZM2G052546_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 5
---gtgctcgtcgcatccttctttagacagaaatatcgctccctaccc------ctgtctgattatc----tgcattcatgtg-cagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA
    | |   |   |  |||   |    |||| | |   ||| | |           | ||||| |     | | | ||  || |||||||||   |||||||| ||||||||||  ||||| || |||||  | || ||||| || |||||||||||||||||
gtgataccatttctactctttaattaggagaagtttttttcctttctaagaagatcatttgatttttgtttttcctccaaatggcagAGTCCAGAAGATGTTGACAAGCTTCGGAGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA
















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|148952817|gb|EC898809.2|EC898809
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|148970824|gb|EE021591.2|EE021591
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|15427195|gb|BI543017.1|BI543017
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|21621474|gb|BQ619480.1|BQ619480
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|67023551|gb|CO452300.1|CO452300
EST:     CAATTTCTTACGCCCANACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACCTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: CAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|211183157|gb|FL428740.1|FL428740
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|71435430|gb|DR816480.1|DR816480
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|76290045|gb|DV029613.1|DV029613
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|211478786|gb|FL377818.1|FL377818
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|76914764|gb|DV165677.1|DV165677
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|149081546|gb|EE170685.2|EE170685
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|148967268|gb|EE018472.2|EE018472
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|211266638|gb|FL405762.1|FL405762
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|148934585|gb|EC878634.2|EC878634
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
EST: gi|91876121|gb|EB406078.1|EB406078
EST:     TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG                         AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC
genomic: TGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAGgtgctcgtcg ... tcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagacagaaatatcgctccctacccctgtctgattatctgcattcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA
                             gtctgat  putative branch site (score: 4)
       agaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctcgtcgcatccttctttagacagaaatatcgctccctacccctgtctgattatctgcattcatgtgcagAGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA