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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgctggttcggttaacacccttctgtatgctttacattcataagattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

Basic information

species Zea mays
transcript GRMZM2G179308_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
-------------gtgagtttgctggttcggttaac---------acccttctgtatgctttacattcataagattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
              | | ||| | | |||  ||||          | |  ||||| |||||||| | |  || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 3
---------------gtgagtttgctggttcggttaacacccttctgtatgctttacattcataagattgc-ttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
                | | ||||     |  | ||  ||        |||     | || ||   ||||| |||  || ||  |||  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtagatttaacttaaatttgtcacgtatgctagtacatactacaatgaaaatccttgattccattgcattggttaaatgggcttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
----gtgagtttgctgg------ttcggttaacacccttctgtatgctttacattcataagattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
    ||   ||| |  |      |||   | | ||    | ||| |   |||  || |    |    || ||   | ||   ||| ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtatttttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
--------------gtgagtttgctggttcggttaacacccttctgtatgctttacattcataagattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
               |||   |  |  | |   | | |     | |||||   |||  |  |    |   ||| ||   | ||   ||| ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtattttgacctgaaacttttcttacatgttatatatgccagtatgacataccatatttgattccattgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 3
gtgagtt-tgctggttcggttaacacccttctgtatgct----ttacattcataagattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||  |  |   |    |    | | | || || ||    | | | || |    |   ||| ||   | ||   ||  ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtaattttaacttaaatttgtcacgtatgcatactacaatgaaaatccttgattccattgcattggttaaatgggcttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
-------------gtgagtttgctggttcggttaacacccttctg-------tatgctttacattcataagattgcttgtatata---taagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
             ||    ||  |  |||    | |||   ||||        | || |    |||  |   |   || |  | |   |||     | ||||  |||||||||||| ||||||||||||||||||||||||||||||||||||||||||
gtaagtactgtctgttgactttttc-ttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
--gtgagtttgctggttcggttaacaccct--tctgt-atgctttacattc--ataagattgcttgtatatat-----------aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
  | | |||| || ||   |||||| || |   |||  |   ||  || ||  ||||| ||   |    || |           ||    || ||||  |||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------gtgagtttgctggt-tcggttaacacccttctgtatgctttacattcat--aagattgcttgtatatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
                              || | |||| |||| || | ||  |   | |  | || |     |      ||  |||  |   |   ||||   || ||||  ||||||||| | |||||| ||||||||||||||||||||||||||||| ||||||
gtaagtgtagtttccttctacttgatcactgtca-tttgttggtatctgctattaggttgccctttggtcagtttgaggtgaaatttgggttggtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT

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|71434755|gb|DR815805.1|DR815805
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAG                         TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAGgtgagtttgc ... tattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgctttacattcataagattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
                                           tctatttt  CT-rich tract
                          ttgtatatataa  TA-rich tract