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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG

Basic information

species Vitis vinifera
transcript Vv13s0019g00840.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 5
-tcttctaatttcttaatgagtaa-tcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaat---catgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 |    |   |  |  ||   ||| ||  |||  |     |     | ||    |          |  || | |    | |||||     |  |||  |  |||||| || |||||||| || || || ||| |||||||| | || |||||||||||||||||||| ||
gtacagtctctattatatatataactctgttaagtccaactattcaaatacaaatcttgttcatgtcctgttctgatatttaaatggatgtataatcatgtacagACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 | | ||| ||   |  |  || |   |   || ||| ||   | ||| |    |||   || |||||  |  |  |||||| |           |||||||| || ||||||||||| ||||| ||| |||||||| |||| ||||| |||||||||||||| ||
gtatactagttctctgctctgtgagagacagtacgttgtttaat-agtttttcctggtatttcatgattttggtgtttgtaatttcc------tgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 | | |||  |   |  |   | |    |  ||| ||||         ||  |||     ||  ||||  |  |  |||| | |       |   |||||||| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||
gtatgctagatctctgttacatgagaggtggtatattttc--------atagttt-----ttcctgatattggtgtttgtgatt------gtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 | | |||  |   |  ||  | |    |  ||| ||||         ||  |||     ||  ||||  |  |  |||| | |       |   |||||||| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||
gtatgctagatctctgctgcatgagaggtggtatattttc--------atagttt-----ttcctgatattggtgtttgtgatt------gtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 5
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 | | |||  |   |  ||  | |    |  ||| ||||      ||| |    ||     || || || || |  ||||   |            ||||||| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||
gtatgctagatctctgctgcatgagaggtggtatattttcat---agtttttcctga----tattggtgtttgtggttgtctgt------------aacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 6
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 | | |||  |   |  ||  | |    |  ||| ||||         ||  |||     ||  ||||  |  |  |||| | |       ||  |||||||| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||
gtatgctagatctctgctgcatgagaggtggtatattttc--------atagttt-----ttcctgatattggtgtttgtgatt------gtatgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 2
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
 | | |||  |   |  ||  | |    |  ||| ||||  | |   | | |||  || |||  ||          |||| | |       |   |||||||| || ||||||||||| ||||| ||| |||||||| | || ||||| ||||||||| |||| ||
gtatgctacatctctgctgcatgagaggtggtatatttt--catagtttttctt--gatattggtg---------tttgtgatt------gtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTAGAGCTAG

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|110700937|gb|EE078028.1|EE078028
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|71860037|gb|DT009092.1|DT009092
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|30132964|gb|CB918303.1|CB918303
EST:     GCATCACCNAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: GCATCACC-AATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|71882833|gb|DT031888.1|DT031888
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110703601|gb|EE080591.1|EE080591
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110690502|gb|EE067657.1|EE067657
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110702160|gb|EE080556.1|EE080556
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|156736486|gb|EV240607.1|EV240607
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|71863746|gb|DT012801.1|DT012801
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACC
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACC
EST: gi|71859225|gb|DT008280.1|DT008280
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110357315|gb|EC920771.1|EC920771
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110723901|gb|EE099257.1|EE099257
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110720753|gb|EE096961.1|EE096961
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110721290|gb|EE098120.1|EE098120
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110727671|gb|EE104694.1|EE104694
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110714087|gb|EE090592.1|EE090592
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110719051|gb|EE096588.1|EE096588
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110687991|gb|EE066031.1|EE066031
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|33407947|gb|CF213574.1|CF213574
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|71862913|gb|DT011968.1|DT011968
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110692310|gb|EE071412.1|EE071412
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|110356627|gb|EC919593.1|EC919593
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|30299440|gb|CB976234.1|CB976234
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
EST: gi|71860871|gb|DT009926.1|DT009926
EST:     ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAG                         ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG
genomic: ATCTTGCTTGTCCTGCATCACCAATTTTCTACAAATACAATCCTGTGAAGgtgtgtatat ... tacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
            cattaat  putative branch site (score: 3)
             attaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - tccctga
- - - - - - - - - - - - - - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgca