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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

Basic information

species Zea mays
transcript GRMZM2G054136_T08
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
gtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
||| | || ||  |||| || | | |   ||       || |  | | ||   ||| | |  |  ||  | ||    |   | |||||| || ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||
gtaaaaaggct--ctatttctattattgactttcggatat-tcatgcccttgctctgaccatattat--gttacttgtatggcagGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 4
------gtatagagacttcctatgtc------cagtgtactctcaacaccatcttttactctgattcttatctgaa----cattcgatatcaattc-tgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
      |||  |    ||  |||  |      |||   ||| | | |  || | |||  | |  ||   || | ||    |||| | |    |  | || ||| ||||| || |||||||||||||| ||||| ||||| ||||| |||||||||||||| ||||| ||||| || ||||  ||||| |||||| |||||||
tttgaggtactgtttttttttataactggactcaggaaacttttagc--caacctttgttattttttcaatgttaaatttcatttgttgcttacccatgcagGAACTCCTTGTTTCCGTGGTTATGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 3
---gtatagagacttc---ctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattct---------gtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
    |  |  || ||    || |  | ||    || |  |   ||   ||  |    ||  |||| || | | | | ||    || |         | ||| ||||| || |||||||| ||||| ||||| ||||| ||||| || ||||||||||| ||||||||||| || || | ||| || |||||| | ||| |
tttatgcaatgatttttagctttaactagaaaccttttcattgcaggattctcagccatgtttatttgcagacttgttaatgttttttgcatttgagcagGAACTCCTTGTTTCCGTGGATATGGAAGGCGCAATGGAGAGCGTAGAAGGAAGTCTGTTCGTGGTTGCATTGTCAGTCCAGATCTCTCTGTTTTGAACCT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 4
----------------gtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                || ||  |  ||  | |||    |    | || |||   ||||||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
ttattaatttttaatagtgtaatgcatttgt-tgttatatcaggtgtctacattttcttttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 5
-----------gtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatat------caattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
           |||||     ||  || || |  ||   | |||  ||||  || |  | |   ||  || | ||  |||  | |       |  |  | ||| ||||| || ||||||||||| || ||||| ||||| ||||| |||||||||||||| ||||| ||||| || ||||  ||||| |||||| |||||||
agtaaggtcatgtatatttgttttttaggtac--tgctttttcataaccaatttatgttattggtccaatgttaaatttctgtttgttgcttacctgagcagGAACTCCTTGTTTCCGTGGTTACGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
-----------gtatagagacttcctatgtccagtgtac----tctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
            | ||   |  || |   |    ||||     | ||    |  || |||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatagagacttcctatgtccagtgtactct-caacaccatcttttactctgattcttatctgaacattcgatatcaattctg-----------tagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
|||          |    |  |    | | | || |  |   ||||    | | |||| | ||    ||   |||    ||||           |||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | |||||||||||||||||||| |||||||  ||||| |||||| | |||||
gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------------gtatagagactt---cctatgtccagtgtactc--tcaacaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                                                                                  | | |  | ||   ||| |   || |||  |   |      |||  |  | |     ||| |||     |||  || |||       | |   ||    |||||| || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||| ||||| || ||| | |||||
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------gtatagagacttcctatgtcc----agtgtac-tctcaacaccatcttttactctgattcttatctgaacattcgatatcaattct-gtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                            || | |||    |   ||    |||  |  | |  |  | |  |    || |||   ||||    ||| |  ||    |||   | ||| || || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||||||||| |||||| | |||||
gtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttcatatttttatgcaagttgggtctatgagatttatt---acactttatgcttatttgagcagGTACCCCATGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGGTGCATTGTCAGCCAAGACCTCTCTGTTTTGAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------gtatagagacttcctatgtccagtgtactctcaacaccatcttttact--ctgattct------tatctgaacatt----cgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                                                             | ||   | |    ||    || |||  |   |  ||||| ||||  |  ||  |  |      |   |||| | |       | |   ||  | ||| || || ||||| || || ||||| ||||||||||| ||| | ||||||||| |||| ||||| ||||| || ||||| ||||| |||||| | |||||
gtgggtttttggtggtatattagtgttggtgcactgaccaccattccttcaagtttaagatggatcacggccagttagaagca-tgttttgctaggaccatgttttgttgccttgtcatagatgatggatgaaaactgttctagttttgcttaagcagGAACCCCTTGCTTTCGAGGATATGGTAGGCGTAATGGAGAGAGGAGGAGGAAGGCTGTACGTGGGTGCATTGTCAGCCAGGACCTTTCTGTTCTGAACTT

upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
gtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                      ||  |         |  | || |  |||   ||||   |    ||| || ||   |     ||||    | ||||| ||||| |||||  | ||  |||||||||| ||||||||||| || ||||||||||| || ||||| || || |||||| ||||  |
----------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgac-cagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT

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|29577181|gb|CB617293.1|CB617293
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|31664073|gb|CD573253.1|CD573253
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|211199269|gb|FL277456.1|FL277456
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|32845854|gb|CD985535.1|CD985535
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|211199270|gb|FL277457.1|FL277457
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGAG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|16137351|gb|BI894216.1|BI894216
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGAG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|148942260|gb|EC887276.2|EC887276
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                ctctgat  putative branch site (score: 4)
                                        atatcaatt  TA-rich tract