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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctaaaaacaatgcattttattctacctttatgttttaactatgcattattaccatttgatgataatttatttcatttcagttgtaaatattaataaaccatactgttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCTGTAATAACCGAGGAAGTGACAG

Basic information

species Zea mays
transcript GRMZM2G005308_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g04010.1 (Oryza sativa), 3'ss of exon 4
gttctaaaaacaatgcattttattctacctttatgtttta----actatgcattattaccatttgatgataattta-tttcatttcagttgtaaatattaataaaccatactg----ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCTGTAATAACCGAGGAAGTGACAG
     | | | |||   ||| || |   | |||  || ||    |  |   ||| ||| | |||||   |  | |  | | |  |||   |   ||  |||  || |    ||    ||  || ||||||| |||||| || || |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| || |
--gtaatatataatatgttt-atccattcattagtttctagaacaaaacagatttttaac-tttgaaactgttctggtattaaatcatcagctcatggtaaagaaaccacttgaaattttcttgtagGTTAATGCTTCCAGCAGACCCAAAAACAGTGCTCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCAGTAATCACTGAGGAAGTCACTG

upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g04200.1 (Oryza sativa), 3'ss of exon 4
gttctaaaaacaatgcattttattctacctttatgtttta--actatgcattattaccatttgatgataatttatt-tcatttcagttgtaaatattaataaaccatactg----ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCTGTAATAACCGAGGAAGTGACAG
     | | | |||   ||| || |   | |||  || ||  || |  ||   ||   | ||     |  | |  | | |  |||   ||  ||  |||  || |    ||    ||  || ||||||| |||||| || || |||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| || |
--gtaatatataatatgttt-atccattcattagtttctagaacaaaacaaagttttaactttgaactgttctgctattaaatcatcagttcatggtaaagaaaccacttgaaattttcttgtagGTTAATGCTTCCAGCAGACCCAAAAATAGTGCTCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCAGTAATCACTGAGGAAGTCACTG

upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g08620.t01 (Vitis vinifera), 3'ss of exon 4
-------------gttctaaaaacaatgcattttattctacctttatgttttaactatgcattattaccatttgatgataatttatttcatttcagttgtaaatattaataaaccatactgttcttttt------agGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCTGTAATAACCGAGGAAGTGACAG
              |||| | |    ||  ||  |    |  |  || | || |  |||||  | |    ||||||   ||| | | |  ||| |  | | ||| || | |   | |||| |  |||||      |||| |||||| |||  ||||| || || |||||  ||||||| || || ||||||||||||||||| |||||| | |||||||| || ||||| || ||||
gtaaccttttttgtttctgacatttttgtgttagagatgaattacatttattcaa-atgcaa-agtgtgctttgatatgaatgtgtgtt-tttaaaatatgaat-ttgacactgcttactttggtttttgattgcagGTAACTGCTGCTAAAAGGCCAAAGAATAGTGCTTTAGAAGTTGATCTAGATTTTGAGCACAATGTGAGACCTCCTCCTGTAATCACAGAGGAGGTTACAG

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|60347217|gb|DN214190.1|DN214190
EST:     AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAG                         GTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
genomic: AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAGgttctaaaaa ... ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
EST: gi|9255313|gb|BE345781.1|BE345781
EST:     AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAG                         GTTACTGCTTCTAGGAGGCCCAAAAACAGT
genomic: AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAGgttctaaaaa ... ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGT
EST: gi|31363813|gb|CD448168.1|CD448168
EST:     AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAG                         GTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
genomic: AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAGgttctaaaaa ... ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
EST: gi|71764578|gb|DR962515.1|DR962515
EST:     ATGCAGGGAGAG                         GTTACTGCTTTTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
genomic: ATGCAGGGAGAGgttctaaaaa ... ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
EST: gi|31351205|gb|CD435562.1|CD435562
EST:     AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAG                         GTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
genomic: AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAGgttctaaaaa ... ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
EST: gi|40303495|gb|CK347882.1|CK347882
EST:     AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAG                         GTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT
genomic: AAATGGAGAAAGCTAATCTTGAACCCAGCACGTGGACCATGCAGGGAGAGgttctaaaaa ... ttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataatttatttcatttcagttgtaaatattaataaaccatactgttctttttagGTTACTGCTTCTAGGAGGCCCAAAAACAGTGCCCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCTGTAATAACCGAGGAAGTGACAG
                           tattaat  putative branch site (score: 2)
                                          ctgttcttttt  putative PPT
     tttatttcatttcagt  TA-rich tract