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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctcttcttcatatattttttattttattgaagtgcttcagcaacccttttgttgtttgttgggcttctggcttttatacgcattgtcttgagattggttattccagttcaatcaaacactgtttgacaagaacacttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG

Basic information

species Vitis vinifera
transcript Vv03s0091g00740.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
gtaagcatctcttcttcatatattttttattttattgaagtgcttcagcaacccttttgttgtttgttgggcttctggcttttatacgc-attgtcttgagattggttattccagttcaatcaaacactgtttgacaagaac----acttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG
              |  || ||  || |  | | |||  ||  ||     |    |  ||   |||  |  ||     ||  ||||    | ||| |      |  | || ||  || |||       ||||||| | ||      |  |     || ||||||||||| ||||||| ||||| ||||||||||| || ||||||||||||||| | ||||| ||||
-------------gtgaatttaccttgtgatgtgttg--gttattgttatatttatcagtaaattgaagtactgtaaactagtatatttgaatgtttattaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G303631_T01 (Zea mays), 3'ss of exon 3
--gtaagcatctcttct-tcatatatttttta-------ttttattgaagtgcttcagca-acccttttgttgtttgttgggcttctggcttttatacgcattgtcttgagattg-gttattccagttcaatcaaacactgtttgacaagaacacttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG
  | |   | ||    | | || || ||| |        |||||||       |  |||| ||   ||| || |||         | | |  |       |||   ||||  ||      | |    | |   |     |  ||         |  |  || || ||||||||||  ||||||| ||||| ||||||||||| || ||||||||||||||  | ||||||||||
gtgaagtgacctagcatattatgtagtttgtcgtggagcttttattagtaaaataaagcacacagatttattttttaaaatataacagtcactgcagactatttcattgaccttttaccgtccttcattatctatgagttaatttgtgctgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC211785.2_FGT003 (Zea mays), 3'ss of exon 1
gt-aagcatctcttcttcatatattttttatttta----ttgaagtgcttcagcaa--cccttttgttgtttgttgggcttctggctttta-tacgcattgtcttga-gattggttattccagttcaat---caaacactgtttgacaagaacacttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG
|| |||   |    | |  ||| |  ||| |  |     ||  | |  |  |  ||  | |   | ||  || ||     | |  |  | | | |  | | | |    ||    |||      |||| |    |     |  ||         |  |  || || ||||||||||  ||||||| ||||| ||||||||||| || ||||||||||||||  | ||||||||||
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacactcactgcagactatttcattgaccttttaccgtccttcattatctatgagttaatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G328265_T01 (Zea mays), 3'ss of exon 4
---------gtaagcatctcttctt-catatattttttattttattgaagtgcttcagca-acccttttgttgtttgttgggcttctggcttttatacgcattgtcttgagattg-gttattccagttcaatcaaacactgtttgacaagaacacttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG
            ||||| |  | |    | |  |     |||||||       |  |||| ||   ||| || |||         | | |  |       |||   ||||  ||      | |    | |   |     |  ||         |  |  || || ||||||||||  ||||| | ||||| ||||||||||| || ||||||||||||||  | ||||||||||
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacagtcactgcagactatttcattgaccttttaccgtccttcattatctatgagttaatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAAGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

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|30299749|gb|CB976543.1|CB976543
EST:     CAAATGCCGATTCTGACAATCCTCTTCTGAAAGAAGAGCAAGATGCTCAA                         GTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTG
genomic: CAAATGCCGATTCTGACAATCCTCTTCTGAAAGAAGAGCAAGATGCTCAAgtaagcatct ... cttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagattggttattccagttcaatcaaacactgtttgacaagaacacttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG
                               gtttgac  putative branch site (score: 4)
                                           cacttcct  putative PPT
                    aatcaaa  TA-rich tract