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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG

Basic information

species Vitis vinifera
transcript Vv08s0007g04980.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 3'ss of exon 4
---gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
    | |  ||| | |  |   |       ||  |  ||| | | | | ||    | ||     ||  || | |  ||     |   | |  |||         | | |    |   | |   ||||  |   |  |   |    ||  |||| |||||||| || ||||| |||||||||||||| ||||| ||||| ||||| || || || || ||||| ||||| |||||
gtaattttcttgttcccttgtttagttgctcttcaaatct-cgatagacttg---ttatgtccaatcctcatgcccatagacctttcact-tattgatgtccctagactcccga---taaacctattacttactacagtttgggattatagGTTGGTCAAGAGCAGTTCTCGCCTAGTTCACCTGGCTGGCCTCCTTTCATGAGGGTCAATCCTATATTGGACTGGTCATACAG

upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G381933_T03 (Zea mays), 3'ss of exon 4
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcct--catactagattatcttccagatttctgtaagattgcattagaagattcaaag-tgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
||  ||||  |  | ||||         |   |||   | ||   ||   |||    |||   || ||  | |  ||     |   | | | ||| |   ||   |  | |      || |  ||   | | |||| | || ||     |||| ||||||||||| |||||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||| |||||
gtg-attt--tcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgattatgcccatggtgttcccagttccttacagttttggtatctcactgaactttgagtaaacacaattttgaaatgat-----agGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATGAGGGTGAATCCAATCTTGGATTGGTCATACAG

upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G149609_T01 (Zea mays), 3'ss of exon 4
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatacta-gattatcttccagatttctgtaaga--ttgcattagaagattcaaagtgataagtgttagtatatttatatttttaacatta--tcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
                                     |  || |   |||  ||  |  | |  |  ||  || | |    | | |  ||   || || | ||||      |   || || | || |     | | ||    |  |  || |||| |||||| || | ||||| ||||| || || || ||||| ||||| ||||| ||||||||||||||||||||||| |||||
-------------------------------------gtgacttcccttgaatcgaatgacgcctgcctgacataatcgaatgacaatttttttttgagggttca------ttgatggtaatctaatcgcggtgtgaatgaaaattgctgtagGTCGGTCAACAAGAGTTCTCCCCTAGCTCGCCCGGCTGGCCTCCTTTCATGAGGGTGAACCCAATCTTGGATTGGTCCTACAG

upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G028010_T01 (Zea mays), 3'ss of exon 5
----------gtatatttgatgctct-acctcaaaaagctata-tgtc----tgctaca--tattttgcctca--tactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattat-cttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
           |  |||   |||||     | |     ||  | ||||    | |||||  | | | |    |  || || | |   |       ||||| || |||      |  |  |  |  ||| | ||| | ||| |||    | |  || |  || |||| |||| |||||| || | ||||| ||||| || ||||  ||||| ||||| ||||| |||||||| |||||||||||||| |||||
gtgactccccttgaattgagtgctcccgttttagtctacttcactgtcgtcattctacacctctatcgatctagctagtatactggttcatgccattctgcaacattttgggggccgggttca--tgacatgtgatggta-attgcggtgtggaaaaaaatacttgtagGTTGGTCAACAAGAGTTCTCCCCTAGCTCGCCTGACTGGCCTCCTTTCATGAGGGTGAACCCTATCTTGGATTGGTCCTACAG

upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
                                          ||  |||   || |  || |  |      | ||||   ||  || |  | | || |     | |  | |    |  |||   ||  | | |     || ||| ||||| ||||||||||||||||| |||||||| ||||| ||||||||||| ||||| ||||| || || || |||||||| |||||
----------------------------------------gtatgcttttgttctt--taaacca------atatttgattaccatggtttaataaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG

upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
                            ||| ||| ||||     |||   |  ||| |  |||| | |   | |||    || | || | ||      |     |  ||  | ||  || || | |  |  ||       ||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||  |||| || || || |||||||| |||||
---------------------------gtatgtgtttgctc----tttaaaccaatatttaattaccat---ggtttaatgaaaactggacta------ttggcatatta--tattcatacatgtgtgctccta------ccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG

upper sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttc--tgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
                                                          ||| ||  |||| |   ||   | | |   | ||   | | ||     ||||||       |  |  |||  || ||||     | || ||||| |||||||| ||||||||||||||||||||||||||||| || |||||||| ||||| || || ||||||||||| |||||
--------------------------------------------------------gttagcttcacttcaaatctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgattgattac-ttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG

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|71855620|gb|DT004675.1|DT004675
EST:     AACCAATCAGAGCTATTTTTCTTGGTGTCCGAATCGGCGATCCTACTGCG                         GTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATG
genomic: AACCAATCAGAGCTATTTTTCTTGGTGTCCGAATCGGCGATCCTACTGCGgtatatttga ... tatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG
                                    ttttaac  putative branch site (score: 2)
                                            ttatctt  CT-rich tract
              ataagtgttagtatat  TA-rich tract