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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA

Basic information

species Zea mays
transcript GRMZM2G311165_T06
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 7
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagc-------aaacatagctgtaa-------attgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
|| ||||||||||||| ||| | ||   | | ||  ||||  ||| |  |         |||  ||  |||||         || |||||||  ||| ||||||   ||  ||||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||| ||||| ||||||||||||| 
gtaagcaccctgtactattagcatc-atatagatcctgcagatttgagcaatgtcagctaaatttaattgtaatggataatctgatattaacctgtttctttttg--tggcagTTGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCA-

upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatt--------tgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
|| ||        |  || |            |   |   | ||||  |       ||| || |   || || | || |||||    | |   |  |||||   |  ||        ||||||||||||| ||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || |||||  | || |||| 
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctc--tatatctattttttcttgtgaaagggttctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA-

upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
-------------------gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgta-agttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
                      |     ||||||  |    || |   ||   | |  || | ||    |      ||  | | | |  | ||||||||||| ||  | |||| |  ||||     || ||||||||||||||||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || |||||  | || |||| 
gtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttga-gctctatatctattttttgttgtggtacat-tcattaatcattaacgggtt-ctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA-

upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
    | |   ||||      |  | |    |  ||||     |  |   | ||    | | ||  |  || |  | | |  |      | | ||| | |||     || ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| || || || || ||||| ||  |||| |||| 
----gtaagttgtaa---agaattttagtaatgttttatggatgctgtcaacatttgtcgttg--acatgatgctgatgtatc-tacatctgttgca-gTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA-

upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
            | |||||||      |  |||| ||   |   ||  |  |||||| |  | || |||| | |||      |  |  |||  |   || |  |||| ||||| || || ||||||||||||||||||||||| || ||||| || || || ||||| |||||||| || || || ||  | ||||| | 
------gttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaat-tatattgatgtta------tattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA-

upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------------------------gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttg----cttttttattgta-agttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
                                                             |   ||     ||   | | ||  | | |    |||  |    |||  | ||  ||   ||||   ||  |  ||  |  |        | || ||  |  ||||| || |||| ||||||||||||||||| || || || || || || ||||||||||| || ||||| || || || |||||||| || ||||| || | 
gtaagatttctttctacccttcaagcacctttataagaatctcatcaagttctgtttgaaatatacaaggactatcatcatccaattctg-tgctttataaggattattatcatccacttctgtgctttactgatagtgtttataaattctgttcatcatccagTTGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAA-

upper sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
--------------------gtgagcac--cctgtacttttaacctctgcagacatt-----ttgcattt---tttaaaagcaaacatagc-----tgtaaattgttattaacg--ggttgctttt-ttattgta-agttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
                     || ||||  ||    |   |    |||   | ||||     ||  ||||   || || || | | ||| |     | |||| | ||   |  |   ||  ||||  || |  |  || |  || ||||||||||||||||||| || ||||||||||| || |||||||| || || || ||||| ||||| ||||| ||||| || ||||| |||| 
gtaagatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtgttctatttagattcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA-

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|149066754|gb|EE286897.2|EE286897
EST:     GCTAATGGCTTATTTATCTTACATGCTAGCTGAA                         AAAGTTCGAGGGTCACAACCAA
genomic: GCTAATGGCTTATTTATCTTACATGCTAGCTGAAgtgagcaccc ... aatgtaacagAAAGTTCGAGGGTCACAACCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
 ttctcac  putative branch site (score: 2)
                                           aaaatgtaa  TA-rich tract