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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG

Basic information

species Vitis vinifera
transcript Vv08s0040g02860.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 3
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG----
                 ||   |  ||   |  |   ||| |   |||| ||            | || |||| || |   |   ||  ||    |||          ||   || |||||||       || | ||      ||  || |||     ||||||||||||||||||||| ||||||||||| ||  | |||||| || ||||  | ||| |||||||||| || ||  |||| || ||||| |||||     
-----------------gtatgtgaatacttccctcatttttttattgcgta------------acttctctctttttaagttcttatgaggtgtatt----------ttgttcacatatgagtcctatattttgcg-----acatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGAGTAA

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
                 ||   |  ||   |  |   ||| |   |||| ||            | || |||| || |   |   ||  ||    |||          ||   || |||||||       || | ||      ||  || |||     ||||||||||||||||||||| ||||||||||| ||  | |||||| || ||||  | ||| |||||||||| || ||  |||| || ||||| ||||| 
-----------------gtatgtgaatacttccctcatttttttattgcgta------------acttctctctttttaagttcttatgaggtgtatt----------ttgttcacatatgagtcctatattttgcg-----acatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G175419_T01 (Zea mays), 3'ss of exon 3
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
             || ||| | |   |  | |   ||    ||     ||  |   |||  | |  |    | || || |   ||||||| |   |  | | ||    ||     |||    |||| |  |  |  |  | |    ||||||  |   ||||||||||||||| ||||| |||||||||||||||   || ||| || ||||  | ||  | |||||||| || || ||||| |||||||| ||||||
-----------gtatgtgtactttactgccctcagttcaattctgcaactgttacctatataatggtggcttgctcatat---tatagaaattgaaaaaaacat----ttgttttaattgtggcattctttattgtgaccct-tggttaattgcaaa-acagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G099186_T03 (Zea mays), 3'ss of exon 4
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
                                                              |  ||||  |  |   |||    ||  |   | |||  | |     ||        | | |     | || ||   ||      ||   ||     ||||||||||||||| ||||| ||||||||||||||    || ||| || ||||  | ||  | |||||||| ||||| ||||| |||||||| ||||| 
--------------------------------------------------------------gatttttaatgttagcttactcgtattatggaaattgaaaaaaacatttattttgcacgtgacattctttattttgtccgatgttttgattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 3
-------------------gtatgtatcaaccatttgttcatctatttctt----tcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
                    ||| | |   | |||| || || |||||| |          ||    |||  ||||  |  |  | | |   |     ||| |   |  || | |    || |||||| || ||     || |  |  |  | || || | |  | |  |  |   | |  |||||| || |||||||| |||||||||||||||||||||||||||||  |||| || ||| |||||||||||||||| |||||||||||||| ||||||
gtaagttgtcaccctttctttatct-ttgtctatttatttatttatttcctaggacttcaatttcttcttatttatt-tgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatg---atttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
gtatgtatcaaccatttgttcatctatttctt---tcctttt--tctcccttgcttatggttatg---gagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
||| ||    ||| ||| ||  ||||||| ||   | |||||  | ||  || ||||||  | ||    |   |   |     |||||   |  || | |    || |||||| ||  |     || |  |  |  | || || | |  | |  |  |  || |   ||||| || |||||||| ||||||||||||||||||||||||||| |  |||| || ||| ||||||||||||| || |||||||||||||| ||||||
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatg---atttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G33270.1 (Glycine max), 3'ss of exon 3
gtatgt-atcaaccatt---tgttcatctatttctttcctttttct-cccttgcttatggttatgg---agtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
||| ||  ||| || ||   | || || |||||||||  |  |||      | || |||  | ||    |   |   | |   ||| |      || | |    || || |||  | ||   | ||  | |  |  | || || | |  | |     || || |  ||||||||| |||||||| ||||||||||||||||| ||||| ||| |  |||| || ||| |||| ||||||||||| |||||||||||||| || |||
gtaagttgtcaccctttctgtctttatgtatttcttttttacttcaatttctcctcatgcctttgctccaaggtggcttttagtatctgctcggaggaattcagttgtaaatgaaggta---agattcg-gtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G35990.1 (Glycine max), 3'ss of exon 3
gtatgtatcaaccatt---tgttcatctatttctttcctttttct-cccttgcttatggttatggagtatttt---tctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
||| || ||| || ||   | || || |||||||||     |||      | || |||  | ||   ||  ||   | |   ||| |   |  || | |    |  || ||| || ||   | || || |  || | || || |  ||||  | | |  || |  ||||||||| || ||||| || |||||||||||||| ||||||| |||  |||| || ||| |||| |||||||||||||||||||||||||| || |||
gtaagtttcaccctttctgtctttatttatttctttttgacttcaatttctcctcatgcctttgctctaagttggcttttagtatctgcttggaggaattcagtagtaaatgatgata---agatttg-gtgtcactttattgg--cttgttcctgacattttgaacagGAATTTAGCGATCCTCGGGATGCTGATGATGCTAGATATAGCTTGGATGGTCGTGATGTTGAAGGAAGTCGTATCATTGTGGAATTTGCCAAGGGG

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ22951 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaag-tcacattatagatggtgttacacaaatatgagcatcccgtt--gttcgtt-cttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
                                                                    ||| ||||  || |   |||||  ||    | |      | || | |     |     ||   ||   ||| || ||  |  |  | |||  |||||||||||||| |||||||| ||||||||||| || ||  || |  | || ||||| || || || |||   || || || || || ||||||| | ||
------------------------------------------------------------------acttcgcctttgttgtacgtagaaactctttcttttctctcttttgctcgctctttgttttctttttctattcatttctctctttcgagtttcgctacagGAATTCAGCGATCCCCGGGATGCTGATGAGGCGAGGCATTATCTCAACGGACGGGACTTCGAGGGACACCGCATGATCGTCGAGTTTGCGAGAAGG

upper sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ30580 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatt-tttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
                                                          |  || |    ||| ||||  || |   |||||     | | |   |  || |       | |   | |    |  |   ||||  |  |  | |||  |||||||||||||| |||||||| ||||||||||| || ||  || |  | || ||||| || || || |||   || || || || || ||||||| | ||
----------------------------------------------------------tcaagcacgacttcgcctttgttgtacgtagaa-----actctttcttttgctcgctctttgttttctttttctattcacttctctctttcgagtttcgctacagGAATTCAGCGATCCCCGGGATGCTGATGAGGCGAGGCATTATCTCAACGGACGGGACTTCGAGGGACACCGCATGATCGTCGAGTTTGCGAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
                                     acttaat  putative branch site (score: 4)
                                           ttttatct  CT-rich tract
                                     acttaattttatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG