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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

Basic information

species Zea mays
transcript GRMZM2G142334_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatt-----tccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
    |||||||| |||  ||||| ||   | | |||  |||| | | ||  |||   || ||  ||||| | |||| | |||    |||| ||     || |||||||||||||||| || |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||||||||| ||||||
---tttgctgatgtgcatctcatatacattcgattagatgtaatgtacc-ctttcgagttttatgtagtgacatat-tgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatata---tatattgtaacctctatttccac-agTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
    || |   | ||    |  || |   |  |||   |   || |   | |||| || | |  |    ||| |    |||  | |       || ||  | || ||||| || || || ||||||||||||||||| || ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
----tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaac----ctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
    |   ||||||    | |||   || ||  ||      | |||   | |||| |  ||   |    ||| |  ||  ||| |     |||   ||    || |||||||| || || |||||||||||||||||||| ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
----tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
----tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgcc---atttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
    | | |   |  ||||| ||     | ||||   |  |   | |||| |    || |  |   ||| || | ||   ||| | ||  ||  |||  |     || ||||| || || || ||||||||||||||||| || ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttgg-actatggtatgt-ttcaaatatctgct-----agCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
---tatgt-tgc-tgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
   ||||| | | ||||||    | ||| | || |   |||| |  |   |   ||   |    ||    |    ||   | |  |||  |   ||| | | ||| ||||| || || || |||||||| |||||| |||| ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ctttatgtctacatgattttgtgcacatttttttt---ttaatttcatggttttatagatactgatcaaatttggatg-gtgttatgttgctcatatcttc-cagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
--------tatgttgctgat-ttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
        | ||| |   || |||    || |  |||  |    |||| |   |||| ||| ||||||     || |||||  ||     ||  |||  |||   ||||||| || || || ||||| || ||||||||| ||||  ||||||| |||||||||||||| ||||| || |||||||||||| ||||||||||||| |||
ttattctctttgtcgaaaatcttgttgatcctaaatttca---caact-tgtattgc-attgttttgttccttgtggtaatgaat----cgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
--tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
   | ||| ||       |   ||  |  |  |  ||| ||  | ||    | |||  |  ||   ||  |  |    ||| | |  |   |||      || || || || |||||||| || |||||||||||||| || |||||||||||| ||||||| ||||||||||||||||||||| ||||||| |||||| | 
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataatt--agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 6
-tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggt-agtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
  |||  ||    ||  ||    | |  |  |   |  ||| |||||   | |   |||||     | | ||   ||   ||| || ||| |  |||   |||||||| |||||||| ||||||||||||||| | || ||||| ||||||||  ||||||| ||||||||||||||||||||| ||||||| |||||||| 
acatggagccatattatccacactattctacatactgtctgcacttt--tagtcacttgtaagaaattaatagactactaattttatcctttcattctcaagTGATGGAGAGACATTCATATCAGCTGATGATCTACGCATAAACCTTTGGAACCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTGAAGCCTACT

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
tatgttgctgatttgcccctcatgt--attgtagcttaactgtactttgccatttttttgt-attgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
       ||  | ||      |||   || ||| |||   | |  | |   ||||   |   |||  ||   | | |    |||||   |||| | ||  |||||||||||| ||||||||||||||||||||| |||| ||||| |||||||| |||||||| ||||| ||||| ||||||||| ||||||| |||||| ||
-gaaagactattatggaaacaatgctaatggtaacttgtttat-ttctcttatttgggtacgatttagtgaaattttgctgattgtt-tctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 6
tatgttgc-tgatttgcccctcatgtattgtagcttaactgtactttgccatttttttg-tattgggtagtaatata-tatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
   |||   | |  ||    || || |||| |   |  |  |    |  ||| ||  || |||||     | |  ||  |     |  | | |   |  | ||||||||||| || |||||||||||||||||| | ||||||||||| ||||| |||||||| |||| |||||||||||| ||| ||||||| |||||| ||
---gttatattagctggatgtcctggattgcatggtctccttttgctaacatattcatgatattgacagatcacttaacactccttttcttttccatttatagTGATGGTGAAACTTTTATATCAGCTGATGATCTCCGGATAAATCTCTGGAACTTGGAAATTAGCAGTCAAAGTTTCAACATTGTTGATGTGAAGCCTGCA

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|6020391|gb|AW065319.1|AW065319
EST:     GTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG                         TGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAA
genomic: GTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAGgtccttcaca ... atttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
                                  ttgtaac  putative branch site (score: 2)
                                        cctctatttcc  CT-rich tract
                    tagtaatatatatatt  TA-rich tract