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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA

Basic information

species Vitis vinifera
transcript Vv17s0000g00690.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 12
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
        || | || ||| ||     |||| |||     ||||      |||| | || |     ||||||       |||| ||| |  || |   | | ||||| ||||||||| ||||||| |||||||| | |||||||||||| || || || ||||| || || ||| | |||||||| ||||| || ||||||||||| 
---gtacgctctctctccacat-----gcattggcacacctgtgt-----gtggataagga-----cttttag------ttctgaca-ctcgttt---tctttgcagCATGTCTGTTGTTGAGGAAAGCTTTGAATATCTTGATGCACCAGTTGAGAGAATTGCTGGAGCTGATGTACCCATGCCCTATGCTGCCAATCTTGAGAGG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 11
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
||   |  || |  | ||    ||    |     | |  || | ||     | || |      ||| |  |  ||        |  || ||| ||       ||||| ||||||||| | ||||| |||||||| | |||||||||||| ||||| |||||||| || || ||| | |||||||| || || || || |||||||| 
gtcggccactctccctccctccctccttc-----ccaatgtataatgt--atagtctgcgtctctcgtaatgggt--------tgaaatgtgcct------ttgcagCATGTCTGTTGTAGAGGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G02380.1 (Glycine max), 3'ss of exon 12
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgt-ctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
|||    |||||  ||  || |   |    ||   ||  || |  || ||||    ||     ||| |   ||  ||         |  |||| ||    ||   ||| |  ||||| ||||||||||| |||| || ||| |||||||| || || || ||||| ||||| ||| ||||||||||||||||||||||||| || |||
gtttatctctttg-cattaatttgtt--tttgtatgaatgtatcttactggt----taa----ctcttggcaatcatg--------agtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTAGATGCACCGGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
gttaccttctttttcaccaaatctatg-gcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgt-ctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
       | | | ||   | ||  ||  |  |  |   |  ||| ||  |  ||||| |     ||| |   ||  ||         |  |||| ||    ||   ||| |  ||||| ||||||||||| |||| || |||||||||||| || || || ||||| ||||| ||| |||||||||| |||||||||||||| || |||
------gtttatctctttacattgatttgtttttgtatgaatgt-atcttactggttaa-----ctcttggcaatcatg--------agtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
|||    |||||  ||   | |   |    |    ||  || |  || ||||    |     |   | | | ||| | |   |  |             ||   ||| |  ||||| ||||| || || |||| || |||||||||||| || || || ||||| ||||| ||| ||||||||||||||||||||||||| || |||
gtttatctcttta-cattgatttgtttttcta--tgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctc-------------ttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 13
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
          ||  |  ||| ||  |         |||    |  ||      |  | | ||  |  ||||||  |      ||| |   | || | | |    ||||  ||| ||| | || |||||||||   |   | |||||||| ||||| ||||||||||| || ||| |||| ||||| |||||||| || || ||||||
---------gttaacttcaattccttaattcaatagagatcttattatcacctggattgtataatagttttaaa-acacggattaaactttttccgtaatggatcagTGCGTCGGTTGTAGAAGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA
                           ttcttac  putative branch site (score: 2)
                                              tttctgc  putative PPT
               ttttaagtatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT