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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaccgattgggcttctctacttcattttttcctttcccttttcttctagtcaactcacaataatcaatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT

Basic information

species Vitis vinifera
transcript Vv13s0067g00220.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 3'ss of exon 2
gtaagccaccgattgggcttctctacttcattttttcctttcccttttcttctagtcaactcacaat-aatcaatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT---
                           | | | | |  |    ||       |||| |   ||  ||  | |||| |  ||  |  |||      |    ||    ||   | |  ||  | || ||||||||||||||||| || || |||||||| || || || || ||  | |||||||||||||||||||| || ||||| ||||||  || ||  | |    
-------------------------tattactgtatgataagtctacatcattagtgaggacatgattgagcaatggcact--taattacaagcactaactcccg-ctgcaatttgctggttctgcagTGGATCTTCTGGGTTGGCCCCTTCATTGGCGCTGCCCTTGCTGCCATCTACCACCAGGTGGTCATCAGGGCAATTCCATTCAAGAGCAGGTCGTAACCTG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
gtaagccaccgattgggcttctctacttcattttttc-ctttcccttttcttctagtcaactcacaataatcaatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT
                     |  |   ||| | ||  ||     |  | |  || |  |  ||   | |    |  |  |  | |  | |  | | | || |   || | | ||  |     | ||||||||||||||||| || || |||||||| || || || || ||  | |||||||||||| ||||||||||||| || ||||||  || ||  | | 
---------------------tagatggcatgtattaactaatgatcctttgttaatgcatgcatgtttaatcctc-tattggtaccgaggagt-cgtgttataacctatgattgttt-----tgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA-

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G392975_T02 (Zea mays), 3'ss of exon 3
gtaagccaccgattgggcttctctacttcattttttcctttcccttttcttctagtcaactcacaataatcaatagtgctaatgcttatggttgcctt--ttcttttcttttactgcctcat--gctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT---
                             |  | |   ||   ||| ||    ||    ||       ||| ||   |||  |    ||   |||| |      || || || ||     ||    | ||||||||||||||||| || || ||||| || ||||| || || ||  | |||||||||||| ||||||| ||||| || ||||||  || ||  | |    
----------------------------tagctgtgtgttaggcttatcacgaag---gcttgtctccatctatgtagcttgtctccatctgtgccataacctcttcctgtttctatacgattgtttgcagTGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTACCACCAGGTGATCATCAGGGCCATCCCGTTCAAGAGCAGGTCTTAAGCTG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 3
gtaagccaccgattgggcttctctacttcattttttcctttcccttttcttctagtcaactcacaataatcaatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT--
                                                                         | ||    ||   |    |  ||| ||| | | | |    |  |  |  | ||||||||||||||||| || || ||||| || ||||| || || ||  | |||||||||||| ||||||| ||||| || ||||||  || ||  | |   
------------------------------------------------------------------------cttgtctccatctgtgccataacctcttcctgtttctatacgattgtt--tgcagtggatcttctgggtcggccccttcatcggcgccgccctggctgccatCTACCACCAGGTGATCATCAGGGCCATCCCGTTCAAGAGCAGGTCTTAAGCT

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|351019993|gb|FQ439810.1|FQ439810
EST:     CTGGGTGCGGCCATCATCTACAAACAAAGGACCACGCATGGGACGACCAC                         TGGATCTTCTGGGTGGGACCATTTCATTGGGGCCGCACTACCAAGCTT-AT
genomic: CTGGGTGCGGCCATCATCTACAA-CAA-GGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATT-CATTGGGGCCGCACTAGCA-GCTTTAT
EST: gi|110689996|gb|EE066710.1|EE066710
EST:     GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCAC                         TGGATCTTCTGGGTGGGACCATT
genomic: GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATT
EST: gi|33409723|gb|CF215350.1|CF215350
EST:     GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCAC                         TGGATCTTCTGGGTGGGACCATTCA
genomic: GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATTCA
EST: gi|161720336|gb|FC071189.1|FC071189
EST:     GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCCC                         TGGATCTTCTGGGTGGGACCATTC
genomic: GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATTC
EST: gi|33409719|gb|CF215346.1|CF215346
EST:     GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCAC                         TGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATAC
genomic: GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATAC
EST: gi|161713874|gb|FC062564.1|FC062564
EST:     GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCAC                         TGGATCTTCTGGGTGGGACCATTCATTG
genomic: GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATTCATTG
EST: gi|33409074|gb|CF214701.1|CF214701
EST:     GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCAC                         TGGATCTTCTGGGTGGGACCATTCATTGGGGGCGCACTAGCAGCTTTATAC
genomic: GCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccacc ... catgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT
    tgctaat  putative branch site (score: 2)
                   ttgccttttcttttct  putative PPT
                        ttttcttttctttta  TA-rich tract