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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttcttttcttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG

Basic information

species Zea mays
transcript GRMZM2G065105_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g50120.2 (Oryza sativa), 3'ss of exon 7
gtacgtttcttttcttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
| | | ||  ||| || ||  || |                || ||| |||  || | ||| |    |  || |  || || |||| ||| || | |||||||| |||||||||||| ||||||||||| |||||||||| ||||||||||| ||||||||||| ||| ||||||||||||| |        
gcaggatttctttgttcttctcaaa---------ccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTG--------

upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
gtacgtttcttttcttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
| | | ||  ||| || ||  || |                || ||| |||  || | ||| |    |  || |  || || |||| ||| || | |||||||| |||||||||||| ||||||||||| |||||||||| ||||||||||| ||||||||||| ||| ||||||||||||| ||| | |||
gcaggatttctttgttcttctcaaa---------ccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG

upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
gtacgtttctttt-cttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatc-agACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
||| |  ||||   | || | ||| |      ||     || |||  |      |    |        | || || |  ||| |    |||||   || |||| |||||||||||||||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||||||| | |||
gtatgaatcttaagcctagtcccaca-----ccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG

upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
gtacgtttctttt-cttatttccagaa---ggaatccattgctttattatgtt--gtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
||| |  |||| | | || | ||| |     ||||| | ||    |  | | |         || |  | |||| || |          | || |   |    |||||||||||||||| |||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||| |        
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtgaactaagggta---------cactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG--------

upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G05720.1 (Glycine max), 3'ss of exon 4
gtacgtttctttt-cttatttccagaa---ggaatccattgctttattatgtt--gtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
||| |  |||| | | || | ||| |     ||||| | ||    |  | | |         || |  | |||| || |          | || |   |    |||||||||||||||| |||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||| ||| | |||
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtgaactaagggta---------cactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTGGTAGGCAG

upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------gtacgtttcttttcttatttccagaaggaatccattgctttattat------gttgtcc--aatcaggaaagctaaaggcaattttgggctattccttcttcat---cagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
                                                |||  ||    |   |||| ||| |    |   || | ||  | |      ||| |||  |  || |  |||| |||    |||     || |     || ||   ||||| ||||||||||||||  ||||||| ||| | ||||| ||||||||||| ||||| || || || ||  |||| || ||||| ||| | |||
gtctgtacctcatcaatattaaatttttttctgattctgacacattgctacaatttagattcaatttacagcacttgtattttacctttctttttgaaggttttcctaagacatggtagcttaag--tgtttcaatttactttacgtttatgttcagACTGAACAAATGAGCAGGATTGTTAACGAGCTAGATTCTATCCATTTCTCAATCAAGAAAGCTTCACAGCTGGTCAAGGAAATTGGTAGGCAG

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|149073510|gb|EE161813.2|EE161813
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|76020464|gb|DT947634.1|DT947634
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|71443470|gb|DR824520.1|DR824520
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|60340573|gb|DN207546.1|DN207546
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|89246761|gb|DY618548.1|DY618548
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTTTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|74237187|gb|DT645101.1|DT645101
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|60353293|gb|DN220266.1|DN220266
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|71770343|gb|DR968280.1|DR968280
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|37374830|gb|CF623807.1|CF623807
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTGGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|60356243|gb|DN223216.1|DN223216
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|71314190|gb|DR793709.1|DR793709
EST:     GGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTAGATTCCATCCATTTCTCC
genomic: GGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|148986505|gb|EE030255.2|EE030255
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|71761831|gb|DR959768.1|DR959768
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|60394000|gb|DN226870.1|DN226870
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|78088594|gb|DV516987.1|DV516987
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|14243604|gb|BG841264.2|BG841264
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
EST: gi|93282965|gb|EB675229.1|EB675229
EST:     AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAG                         ACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC
genomic: AAGAAACCGTCAATGTGGGCACAGAAACTGCAGCTGCTCTGAAAGCACAGgtacgtttct ... tcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG
                  agctaaa  putative branch site (score: 3)
                                     ctattccttcttcatc  putative PPT
                            aatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtttcttttcttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA