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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttattattaccccaaaaaaatcatgtacttgggaatctcatttttttcaggagctttccttgtttcttaggataatttcatcctcacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 18
agttattattaccccaaaaaa--atcatgtacttgggaatctc-atttttttcaggagctttccttgtttcttaggataatttcatcctcacattaattg-cagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
    | ||    |  | | ||  ||| | | || | |  |  |  |||| |  | ||   | ||    |   ||   || || ||| |         ||  ||| |||||||  |||||||||||||||||||| |||||| | || ||||| ||||| ||||| || |||||
----actacctgcttagagaatcatcctctgctagtgccttactgttttatatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 18
-----------------------------------------------------------------------------------agtt--attattaccccaaaaaaatcatgtacttgggaatctcatttttttcaggagctttccttgtttcttaggataatttcatcctcacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                                                                                    |||  |  | |    ||     ||  |||||     |     |         | |  |  |     | |||  |  | ||       |   ||     ||||||||| |||||||||||||| || || || || || ||||| ||||||||||| ||||| || || ||
gtacgtataaagaaaattttgctttattgttgtagttgcaccatgtgcatggaatatccgttacttaccattcatatatgaggtgttagaccaatgtttcatttccatgctgtacaaattaggaaaaaacagaaatgaaattaacacaaatccttttggcacttgtgaatgcttgtttcaaccagGTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 20
-----------------------------------------------agttattattaccc-caaaaaaatcatgtacttgggaatctcatttttttcaggagcttt----ccttgttt---cttagga----taatttcatcctcacatta----attgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                                               |  || |||  |    || |||       | |  | ||  || |||  ||  || | |         |||||   || || |    | |||||   | |  |||     ||||||| || || |||||||||||||| |||||||| |||||||||||||| || ||| ||||||| || |||||
gtatgtttgcagacttgtaatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcagATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATACTTGGATGTCATTCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 26
agttattattaccccaaaaaaatcatgtacttgggaatctcattttt-ttcaggagctttccttgtttcttaggataatttcatcctcacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                              | |   ||    |||    |||| || | |   | ||||          | |   ||    ||| |||||| ||  | |||||||||||||| |||||||| |||||||||||||| || ||| ||||||| || |||||
----------------------------gttagaagatgctgtttaaactcagtagttat---tatttccc--------tcccctcttgtctta-ttgcagATCGTGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATACTTGGATGTCATTCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 30
----------------------------------------agttattattacccca----aaaaaatcatgtacttgg--gaatctcatttttttcaggagctttccttg---tttcttaggataatttcatcct--cacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                                         | || |  |||  ||    |||||| |  || | |||  | | | | |  | || |  |   ||        |||  |    | |||| ||  |  |   |  ||||||| || || || |||||||| || |||||||| ||||||||||| || |||||| | |||||||| |||||
gtatgtcacaaacttgtaatttgtcttatttccagttgaatgctactggtacatcagataaaaaaaaccagtgcgtggtgggagcacgtgctgtttaaaaatgttttaaacacttttgttattttattttattttgccttttctattgcagATCCCGCAATAAGGACAAACTTAGGTATCGTTATCCTCGTGGAGAGTCTTACTTAGATGTTATTCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 19
----------------------------------------agttattattaccccaaa---aaaatcatgtacttg--ggaatctcatttttttcaggagctttccttgtttcttaggataatttcatcctcacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                                         |  | |  |||   | |   |||| || || ||||  || | | || |  | ||   |  | |  ||      ||   | |||| ||  |    ||  |||||| || || || |||||||| || |||||||| ||||||||||| || |||||| | |||||||| |||||
gtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgt--ttaaacactattcttattttattttat--tttgttgcagATCCCGCAATAAGGACAAACTTAGGTATCGTTATCCTCGTGGAGAGTCTTACTTAGATGTTATTCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: PP1S414_24V6.1 (Physcomitrella patens), 3'ss of exon 19
-----------------------------------------------------agttat-----tattaccccaaaaaaatcatgtacttgggaatc--tcatttttttcaggagctttccttgtttcttaggataatttcatcctc--------acattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                                                     |||| |     ||  | | |  ||| |  |   | | |  | |   |||     |  || |  | |  |||| | |   ||||  || ||  |         |  ||  || |||  ||||||||   || || ||  | ||||| ||||||||||||||||||||| |||| || ||||||||
gtaagtatcattttttggacaattgtacagttgctgaacactacaatgatctgagttgtggatctagcagcacctaaacagtacccattcgctacttcttcaagaagtggagaatgtatttttgtgtttggcgataggttgatgtttttgaaattatctttgtttcagAGCACGTAAGGCAGATAAACTCCGCTATCGCTATCCTCGTGGTGAATCTTACTTGGACGTCATCCAAAG

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|352764397|gb|FQ472754.1|FQ472754
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71882349|gb|DT031404.1|DT031404
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|352769630|gb|FQ468558.1|FQ468558
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71888454|gb|DT037509.1|DT037509
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|352768928|gb|FQ468119.1|FQ468119
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCT--GGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71889378|gb|DT038433.1|DT038433
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71887336|gb|DT036391.1|DT036391
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71887343|gb|DT036398.1|DT036398
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71890359|gb|DT039414.1|DT039414
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|27581545|gb|CB004240.1|CB004240
EST:     GATGGAATGACATATGAAGAAATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|34362375|gb|CF403960.1|CF403960
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|110360631|gb|EC923892.1|EC923892
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|110415443|gb|EC981352.1|EC981352
EST:     GATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|77581485|gb|DV219679.1|DV219679
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|352781433|gb|FQ468277.1|FQ468277
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71888451|gb|DT037506.1|DT037506
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71881182|gb|DT030237.1|DT030237
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|71885715|gb|DT034770.1|DT034770
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|27582400|gb|CB005095.1|CB005095
EST:     GATGGAATGACATATGAAGAAATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|352774206|gb|FQ474729.1|FQ474729
EST:     GAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
EST: gi|352768854|gb|FQ468045.1|FQ468045
EST:     GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA                         GTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA
genomic: GATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcat ... ttaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcaggagctttccttgtttcttaggataatttcatcctcacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG
                            ataatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttattattaccccaaaaaaatcatgtacttgggaatctcatttttttcaggagctttccttgtttcttaggataatttcatcctcacattaattgcagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG

- - - - ttacccc
- - - - - - - -aaaaaaa
- - - - - - - - - - - -catgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcctc