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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA

Basic information

species Vitis vinifera
transcript Vv18s0001g01020.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
----------------------------------gtcagtaat-gctaggaagataatgatttattaccaaaagctagggaaaagattttatgtt--atctggatatat-aataaactcttcct-tgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
                                  |  | | || | || |   ||  |  ||||| |  |        ||  ||  || ||| |    ||||   |||| |||||  ||||||  ||| | |   ||||||||| || || |||||||| ||||||||||| ||||||||||| ||||||||||| || || ||||||||||||||||||||||||||||| |||||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------gtcagtaatgctaggaagataatgatttattaccaaaagctagg-gaaaagattttatg---ttatctggatatataataaac-tcttccttgtcttt--catagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
                                                 ||   |  ||    | |||  | | ||||     |   | ||   ||    | |  |||     ||||  | || |  ||||  | | |  ||  |||     |||||||||||| ||||||||||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||||| ||||||||||| || |||||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------gtcagtaat--gctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
                                                             |  |||| |  | |    |  || ||||| |||| |   |  ||    || || |  || ||       | | |||| |  |  ||    | | |   |||||||||||| || |||||||||||||||||||| || |||||||| ||||| ||||| || || |||||||| ||||||||||||||||| || |||||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggca-ttaaatcaatgagtccatctt--taaagtttgtaatcatgtactctgattttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
|| || | ||   |    | | | | || |   |  |||  | |||||| || |           | | || | |       ||  |   ||| ||||||||||| |||||||||||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| || || ||
gtgagcattgactgcctca-agtcaattgtactctgaagagaaggaaaaaatct-----------gttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
|| || ||  ||| || || ||| |||    |   | | ||  | |  |   |||   || |    | | ||   ||    |||||| | ||  ||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||| || || || || ||||||||||| ||||||||||| || || ||
gtgagcaa--ctaagaggacaattattc--cattgagatctctgaagcaatgtttcatttgttcttaaaaatgtcaa----ttccttatattg-atagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtcagtaatgctagga-agataatgatttattaccaaaagctaggg---aaaagattttatgttat------ctggatatataataaactcttccttgtctttcat-agGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
       || |     | | | |  | || ||   | ||     || |        || ||||| || |||      ||  ||   | | | | ||| | |  | |  | | |||   ||| |||||||| |||||| | || || ||||| |||||||| ||||| || || ||||| ||||||||||||||||| |||||||||||||||||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatg-ttatctggatata-taataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
||  |   |  |       |  |    ||    ||  | || || | |   ||| | | ||     ||| |  | || |     |          |  |||   ||| ||||| || |||||  | || |||||||| |||||||| || ||||| || ||||| |||||||||||||||||||| ||| |||| |||||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgcttattagtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataa---taaactcttccttgtctt--tcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
       |  | |  |||   | ||  |  |   |  ||  | |||   | ||   |   |   | |     || |||    |||  |  |  | |   |  ||| |||    || ||||| || |||||| | || || || || |||||||| |||||||| || ||||| ||||||||||||||||| ||||||||||| |||||
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA

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|110706083|gb|EE083673.1|EE083673
EST:     CATTGATAATGGCCCTCCAATTCTCCCAGAGGCTTACCTAGATATTTCTG                         GAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAA
genomic: CATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACCTAGATATTTCTGgtcagtaatg ... tctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAA
EST: gi|161715538|gb|FC069467.1|FC069467
EST:     CATTGATAATGGCCCTCCAATTCTCCCAGAGGCTTACCTAGATATTTCTG                         GAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAA
genomic: CATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACCTAGATATTTCTGgtcagtaatg ... tctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAA
EST: gi|161717869|gb|FC068184.1|FC068184
EST:     CATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACCTAGATATTTCTG                         GAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAA
genomic: CATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACCTAGATATTTCTGgtcagtaatg ... tctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA
                                   ctcttccttgtctttc  CT-rich tract
       attttatgttatctgg  TA-rich tract