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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaggagctactttcaatttcctttccactttgttgctcatattattcttcaggatgatcaccttttattttcataattaaataataaagctaatattggatttgtattttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 4
gtacgaggagctactttcaatttcctttcc----actttgttgctcatattattc-ttcaggatga-tcaccttttattttcataattaaataataaagctaatattggatttgtattt--tttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG
||||         || ||  ||  | |||     | | | |   |   |  |  | | ||   ||| | ||  | |   |  |||||   | | |   | |  ||||   | |||  ||  |  ||||| |||||| |||||||||||||| |||||||| ||||| || || |||||||  |||||||| || ||||||||||
gtactgccctgctctatcggttgtcattctcgtgattgtttcagtggaaacacgcgtgcaaattgagtgactgtctgggtgaataatctga-attggggtttttattctgtgtgttcttggtcgcagGTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 4
gtacgaggagctactttcaatttcctttccactttgttgctcatattattcttcaggatgatcaccttttattttcataattaaataataaagctaatattggatttgtatttt----ttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG
||| | ||| ||  |||  |         |  ||||||    || |     || || |   |    |   || |  ||   |   |  | |   |   ||||  | | |  ||     || ||||||||||||||||| ||| |||| ||||||||||||||| | |||||||| | | |||| || |||||||||||||
gtatgtggatctgtttttgaa--------cgttttgttttgaatttagaaatttagaaatctattgtagaatatggattgctgtgtgttgattttgggattgcgtgtattattcggggtttagGTATATTGACATGGCTGAGACCTTGTGTCAGAAGCGTGCACTTGAAGCTTTTCGGCTGGATCCAGCAAAATGGGGAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 4
gtacgaggagctactttcaatttcctttccactttgttgctcatattattcttcaggatgatcaccttttattttcataattaaataataaagcta-atattggatttgtattttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG
||| | | | ||  |||  | |   ||     ||||    |   | | | ||  ||    || |    || ||        |  ||  |     ||  | |   ||| |    ||   || || ||||||||||| ||| |||| ||||||||||||||| | |||||||| ||| |||| || |||||||||||||
gtatgtgcatctgtttttgaatgtttt---gttttgaatttagaaatttactgtag----attatggattgttggtgagtgttgattttgggtttacgtgtataattcggcgctt---agATACATTGACATGGCTGAGACCTTGTGTCAGAAGCGTGCACTTGAAGCTTTTCAGCTGGATCCAGCAAAATGGGGAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 4
gtacgaggagctactttcaatttcctttccactttgt-tgctcatattattcttcaggatgatcaccttttattttcataattaaataataaagctaatattggatttgtattttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG
                                   || ||    | |||| ||| |  ||| |   ||||  || | |  ||   ||  | ||| |  | ||| || | ||||   | ||||| ||||||||||| ||| | |||||||| || || |||||||||||||| ||||| || ||| | ||||||||||
-----------------------------------gtatgtatttgttatactt-acaatggtttacttt-gttgttagtatatgatgcttaaggttgt-ttgcatct-tattgact-agGTACATTGACATGGCTGAGACATTATGTCAAAAACGCGCATTAGAAGCTTTTCAGTTAGATCCTTCTAAATGGGGAG

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|352776821|gb|FQ472708.1|FQ472708
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|352795184|gb|FQ477294.1|FQ477294
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71862434|gb|DT011489.1|DT011489
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|352764989|gb|FQ473637.1|FQ473637
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71855735|gb|DT004790.1|DT004790
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71854985|gb|DT004040.1|DT004040
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71858517|gb|DT007572.1|DT007572
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71857493|gb|DT006548.1|DT006548
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71858780|gb|DT007835.1|DT007835
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71854655|gb|DT003710.1|DT003710
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|161708846|gb|FC059632.1|FC059632
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|352781776|gb|FQ469074.1|FQ469074
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|110359383|gb|EC920779.1|EC920779
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71858467|gb|DT007522.1|DT007522
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|294966030|gb|GW837397.1|GW837397
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GCATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71855977|gb|DT005032.1|DT005032
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71857388|gb|DT006443.1|DT006443
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|352764283|gb|FQ471263.1|FQ471263
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|352768688|gb|FQ467900.1|FQ467900
EST:     AAGAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71858984|gb|DT008039.1|DT008039
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71859287|gb|DT008342.1|DT008342
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|161713667|gb|FC062807.1|FC062807
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|352765325|gb|FQ466022.1|FQ466022
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71856061|gb|DT005116.1|DT005116
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
EST: gi|71857262|gb|DT006317.1|DT006317
EST:     AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGA                         GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT
genomic: AATAAATATAGTGAAGGGTATCCTGGTGCGAGATACTATGGAGGAAATGAgtacgaggag ... attttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttattttcataattaaataataaagctaatattggatttgtattttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG
                           agctaat  putative branch site (score: 3)
                                            tattttttc  putative PPT
            ataattaaataataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaggagctactttcaatttcctttccactttgttgctcatattattcttcaggatgatcaccttttattttcataattaaataataaagctaatattggatttgtattttttcagGTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC