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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctcagtttgaatgtgccgctcaacagtttctttactgcatggcagtcgcaatatatggaa...

Basic information

species Vitis vinifera
transcript Vv10s0116g00670.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os03g13220.1 (Oryza sativa), 5'ss of exon 4
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctcagtttgaatgtgccgctcaaca-gtttctttactgcatggcagtcgcaatatatggaa
   ||||| ||   ||| |||||  ||||  | || |||||  ||||||| ||||| || || ||||| ||||| ||||||||||| |||||||| || |||||| |   | | |||  ||| |     ||| |||    || |  |    ||      | | || || |||  | ||||   |        |   |  ||
AAGAACTGTCCATATGGGGAACTATTGGATGTTTCCCAACGATTGAAGACCGCAAGTGAAGTTAATGCTGCCATTCTTACAAGCCAAAGTCATGAGAAAGgttag-cacatgtgctttgatatagtattcatattgagacctaatatcacttggttatgttatcatgtatctacattgcaataccagttttgtgcctataa

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA15G07570.3 (Glycine max), 5'ss of exon 6
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctc--agtttgaatgtgccgctcaacagtttctttactgcatggcagtcgca-atatatggaa
|||||||| |||||||| || || || ||||||||||| ||| | ||||||||||| |||||||||||||| || ||||| |||||||| |||||||| |||| ||  |   | |     |   |      || |  ||  |    ||||| ||||   | |  | |  |  |||    |       || ||   || ||   
TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCTTAAAGACAGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtacttgctgcaaaagtctgtttctgttcatatataatttgggtttgtatgtctggttttaaatctagtttggcactcaattttcacatgaatgtg---

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA13G31720.1 (Glycine max), 5'ss of exon 5
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc----------tttccttctataaatacagcatcttggatgctc-agtttgaatgtgccgctcaacagtttctttactgcatggcagtcgcaatatatggaa
|||||||| |||||||| || || || ||||||||||| ||  | ||||||||||| ||||||||||||||||| ||||| |||||||| |||||||| |||| ||  |           | |  |||||   ||| |  |  | ||  | |  |  |  | | || | |||||   |  |   | ||  |     |              
TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGTTTAAAGACAGCAAGTGAGGTGAATGCAGCCATACTTACTAGCCAGAGCCATGAAAAAGgtttgtgcttgctgcagaagtctgtttctacgcatatataacttggggggttttaaatctagtttggcactcaattttcacacgaatgtgttatttttat-----------

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT1G61150.3 (Arabidopsis thaliana), 5'ss of exon 5
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctcagtttgaatgtgccgctcaacagtttct----ttactgcatggcagtcgcaatatatggaa
|||| |||||| |||   || || || ||  | || || || || ||||||||||| || || |||||||| || |||||||||||||| || ||||| |||   | ||   |  |  | | | ||| |  | |    |  | ||    ||  | ||  |  | | | ||     | | |   |  || ||  || ||    | 
TCTACCTGCCCGGTTAAAGAGCTTCTTGATCTTTCCCACCGTCTTAAGACAGCAAGTGAAGTAAATGCAGCGATTCTTACAAGCCAGAGCCACGAAAAAGgtagcttttgaattttgatgtta-tactggttgtcttttagt-agccacaaaataccatt--ataatctcgagcatcattcattatcaatcttaagattcaaag

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|27579957|gb|CB002652.1|CB002652
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|34546271|gb|CF514503.1|CF514503
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|110702440|gb|EE081156.1|EE081156
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|34544716|gb|CF512948.1|CF512948
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|110415950|gb|EC981891.1|EC981891
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|32246915|gb|CD712734.1|CD712734
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|83275082|gb|DV939178.1|DV939178
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|30323272|gb|CD006534.1|CD006534
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|45770907|gb|CN006759.1|CN006759
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|27578911|gb|CB001606.1|CB001606
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|32459223|gb|CD800397.1|CD800397
EST:     CGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: -GCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
EST: gi|110408401|gb|EC974037.1|EC974037
EST:     AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGG                         ATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC
genomic: AGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttc ... attgaaccagATCCAAAACTTCCCAGTTTGTTAAAGATGCTGATTTGGGCCCAGAACCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctcagtttgaatgtgccgctcaacagtttctttactgcatggcagtcgcaatatatggaa

- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataca