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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

Basic information

species Vitis vinifera
transcript Vv00s1338g00020.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------------------------cag-gaataactgaagtagatttcaatttttttgcttgtctaatttccttatgta-gcctgttctatatatatacaacaatctgattttctc-tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                                                   ||| |  |||      |  | | | |   | |       ||| |    |  || | |   ||| | | | | | |       | || || |  ||   ||||||||||| ||||||||||| ||||| ||| |||| ||| |||| |||||||| |||||||| || || ||||||||||| ||||| ||||||||||||  |
gtaagtatttatagaaatagcgcaatatcctattttatattgtcttatatattggtggtaatgtgttcagagtctaatgtgcatgtactgctagcctgtcctgcacctagtgatttagtgaatgaaagttttttttttttgcctggtggtaatcttgtgatgtgactcagGAATGGCGCACAAAAGCTGCTGGGTATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGTAGTGTGAGCCAACTTGGAACT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgcttgtctaatttcc-----ttatgtagcct----gttctatatatatacaacaatc-tgattttctc-tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                                                   || | |   || |   ||  ||| |  |  |   ||  ||||  ||      ||    ||| |     |||| | | | |       |  | || || |  ||   || |||||||| ||||||||  | ||||||||| |||| ||| |||| |||||||| |||||||| || || ||||||||||||||||| ||||||||||||  |
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgct-agccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------cag-gaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                                                                                     ||| ||||  ||    | ||||  |||  |  | | | ||| |||    | |      | || |   |||||     |  || || | || |    | ||||||||| ||||||||| |||| || |||||||| ||  |||| |||||||| ||||||||| | || ||||||||||||||||| ||||| ||||||  |
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggcta---ttgatta-aatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatat-atacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                                                        | | | |   |       |||||  | |  | |  |||| || |   ||||  | | | |  | | |||  |    ||   ||   |||| | |   |||||||||||||||||||| | || || |||||||| ||| |||| |||||||| |||||||| || || ||||||||||||||||| ||||||||||||   
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttac---tcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------caggaataactgaagtagatttcaatttt-tttgcttgtctaattt-----ccttatgtagcctgttctatatat--atacaacaatctgattttctctgcct--ctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                           ||    |||  | || |  | || ||    | |||     ||  ||     |||| ||     | ||  ||||||   ||     ||     || |  | | |  ||||||||||||||||||||| | || || ||| |||| ||| |||| |||||||| |||||||| || || ||||||||||| ||||| ||||||||||||   
gtaagtgttgtctttctaaaaatattgtgatcttcaattatcacaattctaatcgtagcatttctctatcaagtctgccatagtagattataaaccttctgatctgtatttaatatatttgtattgtgatgcacattgcatttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCTTGATCGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGTAGTGTAAGCCAACTTGGAACA

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G073498_T03 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatat-atacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                                                        | | | |   |       |||||  | |  | |  |||| || |   ||||  | | | |  | | |||  |    ||   ||   |||| | |   |||||||||||||||||||| | || || |||||||| ||| |||| |||||||| |||||||| || || |||||||||||||||                  
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttac---tcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGT------------------

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 1
---caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
       |  || |||   | |||   |  |       | | |  |||   |   |    | |    | | |  |    | ||  | | |   |    | ||| |||||||| || ||| | || || ||||| || ||  |||| ||||| || || ||||||||||| ||||||||||||||||| ||||||||||||  |
tccttttatcaattgactgacattgagaactgcaaagctttatggtttttattcttg---tatctggtgttttcatgtgattcatagtgtactttttacccagAAATGGTGCGCAGAAGTTGCTTGGTATCCTTATTGCCATTGGAGAAGCCGTGGCGTATGTTCTCTCTGGAATGTATGGCAGTGTGAGCCAACTTGGAACT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 1
-------------------------------------------caggaataactgaagtagatttcaatttt-tttgcttgtctaattt-----ccttatgtagcctgttctatatat--atacaacaatctgattttctctgcct--ctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                           ||    |||  | || |  | || ||    | |||     ||  ||     |||| ||     | ||  ||||||   ||     ||     || |  | | |  ||||||||||||||||||||| | || || ||| |||| ||| |||| |||||||| |||||||| || || ||||||||||| |||                  
gtaagtgttgtctttctaaaaatattgtgatcttcaattatcacaattctaatcgtagcatttctctatcaagtctgccatagtagattataaaccttctgatctgtatttaatatatttgtattgtgatgcacattgcatttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCTTGATCGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGTAGT------------------

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G307252_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                                                        |  || |||   | |||   |  |       | | |  |||   |   |    | |    | | |  |    | ||  | | |   |    | ||| |||||||| || ||| | || || ||||| || ||  |||| ||||| || || ||||||||||| ||||||||||||||||| ||||||||||||  |
gtaagtgttgttgggtagtatagacatcaaattctatatgtattggtggatgctttgattatccatccttttatcaattgactgacattgagaactgcaaagctttatggtttttattcttg---tatctggtgttttcatgtgattcatagtgtactttttacccagAAATGGTGCGCAGAAGTTGCTTGGTATCCTTATTGCCATTGGAGAAGCCGTGGCGTATGTTCTCTCTGGAATGTATGGCAGTGTGAGCCAACTTGGAACT

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|351028747|gb|FQ433177.1|FQ433177
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|349832293|gb|FQ420854.1|FQ420854
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|110718605|gb|EE095630.1|EE095630
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGTGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|110689014|gb|EE067912.1|EE067912
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|110701078|gb|EE078295.1|EE078295
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|161717695|gb|FC067907.1|FC067907
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|161721221|gb|FC070727.1|FC070727
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|34549670|gb|CF517902.1|CF517902
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|161718391|gb|FC067285.1|FC067285
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
EST: gi|161713883|gb|FC062862.1|FC062862
EST:     TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTT                         GAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT
genomic: TCAAAGATTATTGAAGTGGACAACAATGTGCGCGAGGATCGTGCTCTCTTgtaagtatcc ... tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT
                                atctgat  putative branch site (score: 4)
                                      ttttctctgcctctc  CT-rich tract
                 tatatatatacaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- ggaataa
- - - - - - - - - - - - - - - - gcttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaacaa