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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacgcactgaagtgtgttactagagttaccacaaatattaagctactggttcctgttctgctttatggagtaagtagtggtttttttttttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G120175_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 6
--acaacgcactgaagtgtgttactagagttaccacaaatattaagctactggttcctgttctgc-tttatggagtaa-gtagtggtttttttttttgctgt-agGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
      ||   || || || |||    ||     | |  | |||   || | |   |  |       |||  | ||||   | |   | |  |||||   |  |||||||||| || || || || ||||||||||||||||| |||||||||||||||||||| || ||||||||||| ||||||||||||||||||
ttctttcgtcatgcagagtattatggtag-----aaaggttttattgtattagcagcattcacatacttacagtgtaacagaataactgtactttttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG

upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G03790.1 (Glycine max), 3'ss of exon 6
--acaacgcactgaagtgtgttactagagttaccacaaatattaagctactggttcctgttctgctttatggagtaagtagtggtttttttttt-tgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
    |  | | | |  |   || ||      |  | | | |     ||  |   |    || ||  | |   | |    | ||   |  ||    |  |  |||| |||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| |||
ttctagagaattcagat---tttctctgtgcattatatacaaagttcttatatatgaaattttggatcaattattcttcactgacatgattgcaatatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
acaacgcactgaagtgtgttactagagttaccacaaatattaagctactggttcctgttctgctttatggagtaagtagtggttttttttt--ttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
   |    |||     | |    | ||||   | | |||| ||  |  ||| ||   | ||  ||  |       |   || || | || |  ||  |  |||| |||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| |||
-agattttctgtgtattatatacaaagttcttatatatatgaaatt-ttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0009g03650.t01 (Vitis vinifera), 3'ss of exon 6
acaacgcactgaag-tgtgttactagagttaccacaaatattaagctactggttcctgttctgctttatggagtaagtagtggt----ttttttttttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
   |  |    | | ||| | ||| || |    |   ||  ||  ||     |   | ||||| |  |  |  |      |       ||||| |  || |  |||| ||||| || |||||||| ||| |||| || || ||||||||||| ||||||||| | |||||||| ||||| || || ||||||||||||
---attcttaaaggatgtttcacttgaatatggattgatgcta--ctggacataaattttctgatcaaaagttttttctctcacaacatttttctgatgtttcagGCTCTTGATACTTTCAACACTGCAGTTGTGTCCCCCATATATTATGTCATGTTCACATCACTTACAATCCTTGCTAGTGTGATAATGTTCAAG

upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
lower sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
------------------acaacgcactgaagtgtgttactagagtt---accacaaa--tattaagctactg-gttcctgttctgctttatggagtaagtagtggtt-----------tttttttttgc---tgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
                  | |||   ||  |   ||| ||| || ||    |||  ||  | | ||  |  |  |  |   || ||||| |||   | |   || |||           ||  |  |  |   || |||| || ||||| || |||||||||||||| ||||| |||||||| || ||||||||| |  | || || || || || |  || |||||||||
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG

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|101381796|gb|EB812955.1|EB812955
EST:     CAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: CAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|60354097|gb|DN221070.1|DN221070
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|78120401|gb|DV538785.1|DV538785
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|76281094|gb|DV020662.1|DV020662
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTTCA-CACGGNCA-TTGTATCTCCAATATATTA
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTT-CAACACGG-CAATTGTATCTCCAATATATTA
EST: gi|148943740|gb|EC888810.2|EC888810
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|149085220|gb|EE174728.2|EE174728
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|76287457|gb|DV027025.1|DV027025
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactggttcctgttctgctttatggagtaagtagtggtttttttttttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
                                     tttttttttttgctgt  CT-rich tract
                                  tggttttttttttt  TA-rich tract