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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC

Basic information

species Vitis vinifera
transcript Vv18s0001g01020.t01
intron # 5
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 5
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
--ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatgaaat-gtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
       |||| |||    | |   ||   | ||  |||  |  |  |||   |  | |   | |  |  || | ||     ||    || ||  || |  ||||  ||||||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| || ||| |||||||||| ||| 
tgaataatctataagtttttgtagtttatatcttttccttgtttgcatgt---agcactgaagtagcggcattgcttaatatgtgtggtaattctttctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
-ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
 |    |  |    | |  |  | ||   || |    | | | |||| |    | |||       ||   || || |   ||       ||| || | |||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||  |||| || || ||| 
accaggttaaatttaacaatgatattgttttctttagtaccctgtttattgagaaattcccatcttgtt-tgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaat---gaaatgtttgtctg-gttgaatattttgttg--tgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
     |||   || |  | |  | ||  |  |    || ||| ||   |||  |||| ||  |||   |   ||||||  |  |  | | ||| ||||   | |||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||  | || || || ||| 
-----tctggcagtgggtctgccctttttagtgttttcttca-ttaccctgtttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 5
--ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatga--aatgtttg---tctggttgaata---ttttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
     |  | | || |  | |||      |    |   ||     |||||   |||  || |   ||      |   ||   | |  || ||     || |||  | |||||||||||||||||||||||| |||| |||||||| ||||| ||||| ||||| ||||| || |||||||||||||| || ||||||||||| || ||||
gtaatttaccataaaaatccttcgtccctccagca-tttcgcagatttgttgaaatgattggttgatttctgcttcctgcattttttttaaaccggtttgtgtctttcagGTTTTGAAAACACCTGTATCATTGGACATGCTTGGGCGCATATTTAACGGTTCAGGAAAGCCGATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACC

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatgaaatgtttgtctggttgaatattttgt-tgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
                                                     | |      ||   |||||    |||   |   | ||  |||    |   | | |||    |    |||   | |   | | |  | ||| | | |||||  ||||||| ||||| ||| |||| |||||||||||||| ||||| || || ||||| || |||||||||||||| || ||| |||||||||| ||||
gtgttactataaaagccttctcctcttttaagcttttggcagattagttaaaattttggttggaagttttctaaaaactaagaggatgcttggttacagtttttttcttgttctttttttgtcattatctgttattggtgtgtgttttcagGTACTGAAAACGCCTGTGTCATTGGACATGCTTGGCCGCATATTTAACGGCTCGGGAAAGCCAATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACC

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggc--aatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
 |  ||   | |     ||||| |||    ||||        ||| ||||  |  |||||     || ||   |||   |  |    | |||  | ||  ||||  | |||||||| || ||| |||| |||||||| || || || ||||||||||| ||||||||||| || ||||| || |||||  |||| || ||||
-ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatt-tcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

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:     GCACTTCTGGAATTGACAACAAATACACAACCGTGCAATTTACTGGAGAG                         GTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGT
genomic: GCACTTCTGGAATTGACAACAAATACACAACCGTGCAATTTACTGGGGAGgtataaagcc ... tgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGT
EST: gi|161717869|gb|FC068184.1|FC068184
EST:     GCACTTCTGGAATTGACAACAAATACACAACCGTGCAATTTACTGGGGAG                         GTTTTGAAAACACCTGTATCACTTGATATGCTTGGCCGCATTTTTAATGGT
genomic: GCACTTCTGGAATTGACAACAAATACACAACCGTGCAATTTACTGGGGAGgtataaagcc ... tgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgaatattttggcaatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC
                                          ttttgtt  CT-rich tract
                                   ttgaatattttgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC

ctctctc
- - - - - - - gcctttc
- - - - - - - - - - - - - - - - - cctcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctgg