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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacattttgattctagctttcaggactatcagctgataggccatgaatcgtacgtagtgattttaacttgcctctgagtacaaattgttttttagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT

Basic information

species Zea mays
transcript GRMZM2G445617_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g52690.3 (Oryza sativa), 3'ss of exon 7
------------------------gtaaacattttga----ttctagctttcaggactatcagctgataggccatgaatcgtacgtagtgattttaacttgcctct---gagtac--aaattgtttttt----------agGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT
                         |  | || ||      |||||||| ||||  | || ||| ||  |     | |||||   ||     |||||||||| |      |||||   | |||  ||||          |||||||||||||||||||||| || |||||||| || ||||| ||||||||||||||||||||||||||||||                            
gtaagacattttaacgtcctgttttttgatatcttatattcttctagctctcagacccattagcagactgctttggcatcgtgtatatgtgatttaacttgctttcatcaagtacttgatttggatttttatgtgctacagGTTCCTAATGTCAAATGGGAGGACGTTGGTGGTCTTGAGGAAGTGAAAAAGGTTATTCTAGATACTATTCAG----------------------------

upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------gtaaacattttgattctagctttcaggactatca--gctgataggccatgaatcgtacgta--gtgattttaacttgcc---------------tctgagtacaaattgtttttt---agGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT
                                                 | | |    || | | | | ||| | | | |  |  |   |||  |   |||   |  ||   |||| ||  |  | ||               | | ||||   ||| || |||   ||||||| ||||| |||||||| |||||||||||||| || ||||| |||||    ||||| |||||| |||||                            
gtagattaagtgatcaggcttttatgatggttttcatgtctgcatttaagcagaacaatttactgttgttttgatgcccaaaaatgtatatatactgcgaaagatgtgttctgtgaattagatgttccacaatgcacagaaattttaagtatggatttttcttttgcagGTTCCGAATGTGAAATGGGAGGATGTTGGTGGGCTTGAAGATGTCAAAAAATCAATTCTGGATACTGTTCAG----------------------------

upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA03G36930.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------------------gtaaacattttgattctagctttcaggactat----cagctgataggccatgaatcgtacgtagtgattttaacttgc------ctctgagtacaaattgtttttt---agGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT
                                                                    ||||||| | |           |||    | |  || | |   ||      |  ||      | ||    |       |   ||||   ||| || |||   ||||||| ||| | ||||||||||||||||||||||| || ||| | ||||||   || || |||||| |||||                            
gtaaattgagtgatcaggcttttatgatggttttcttgtctgcatttaagcagaacaatttactgttgttttgatgccaaaaaatgtatatatagcacggaagacatgttctgggaaaaaaatatgttcctcaatgcacagaaattttgaagtatggatttttcttttgcagGTTCCGAATTTGAAATGGGAAGATGTTGGTGGGCTTGAAGATATCAAAAAGTCAATCCTGGATACTGTTCAG----------------------------

upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------gtaaacattttgattctagctttcaggactatcagctgataggcca----tgaatcgtacgtagtgatttta-----acttgcctctgagtacaaattgttttt-tagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT-
               |      | || |  |  ||     |  | ||   | ||  | ||    || ||  |   | || | |  |     || |  ||   ||    | |||| ||  |||||||| ||||| |||||||| |||||||||||||| ||||||||||| |     ||  | || ||  ||||  ||  |    ||  ||  |  | ||  | 
gtaacattcacagttttcttgctgtggtgttttctcgtttgtttgtctatttatgagacaagtttgcatatttttttgttactggagatgcacataacttaaaggtttatttgtattcgtagGTTCCAAATGTGAAATGGGATGATGTTGGTGGGCTTGAGGATGTGAAGACATCGATATTGGACACAGTTCAACTACCTCTC-CTGCATAAAGATTTATTTT

upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------gtaaacattttgattctagctttcaggactatcagctgataggccatgaatcgtacgtag--tgattttaacttgc--ctctgagtacaaattgtttt---ttagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT
                                                                 | |||  |||| |    |  ||   |  |   |||    |   |  |   || ||   |     |||    | ||    |||||||     ||| |||    |||||||||||||||||||||||||||||||||||||| ||||||||||| |||   |||||||||||| |||||                            
gtaaactgaggagcaatagtagctaaatttgtgccatgatgttacattctgggtttgatcattcagcaaaagttttaa----attttcttgagcaggcagtgagttctcttttcttcctagagaaatctattgctgcctgtatttctgagtctttcttgctttgacctagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTTGAGGATGTGAAGAAGTCGATTCTAGATACTGTTCAG----------------------------

upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 8
-gtaaacattttgattctagctttcaggactatcagctgataggccatgaatcgtacgtagtgattttaacttgcctctgagtacaa--attgt-tttttagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT
 || || |  |  | | ||  | |     | |        | |  |||     | | || |   | |||       | | | ||      |||| |||  || |||| ||||| ||||||||||||||||| ||||| |||||||||||||||| |||||| || ||  | |||                            
ggtcaagaagtctagtgtatatgttgcttcgacagagcatttg--catcccgtgcatgtggcattgttactactattttcaatattgttgttgtatttccagATTCCAAATGTGAAATGGGAAGATGTTGGGGGGCTTGAGGATGTGAAAAAGGCTATTCTCGACACAGTGCAG----------------------------

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|32942888|gb|CF047707.1|CF047707
EST:     CCTTGGAACGAGCCAAGAAACGGAATCGTGCTGCACTGGGCACACCCAAA                         GTTCCTAATGTCAAATGGGAGGATGTTGGTGGGCTAGAGGATGTGAAAAAG
genomic: CCTTGGAACGAGCCAAGAAACGGAATCGTGCTGCACTGGGCACACCCAAAgtaaacattt ... tgttttttagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgaatcgtacgtagtgattttaacttgcctctgagtacaaattgttttttagGTTCCTAATGTCAAATGGGAAGATGTTGGTGGGCTAGAGGATGTGAAAAAGGTTATTCTAGATACTATTCAGGTAAATTGGACTTGATTCAACTGTAAAT
                    ttttaac  putative branch site (score: 2)
                                            ttgtttttt  putative PPT
                                      tacaaattgtttttta  TA-rich tract