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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG

Basic information

species Vitis vinifera
transcript Vv17s0000g04540.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 4
----tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattg-cagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
     |   | |    ||||||||   | | || ||||  |||   | |  |||||   |  | ||     |  | |    |||||  |  ||| || ||  |||||||| || || ||||| || |||||||| ||||||||||| || || || |||||||| || ||||| ||||||||||| ||| ||||||| ||||| |
gtaccatcaaattcctattgttcttctgataatgatcagttcta--agtccaatataa-acatggactgcaaaatgacaaaaatat--attcaactgtttttcagGTTAATCAAATTGGCACTGTCACTGAATCAATTCAAGCTGCTCTTGATTCAAAAGCTGCTGGTTGGGGCGTGATGGTCAGCCACAGGAGTGGGGAAACGG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 4
--------------------------------------tagttactggta-attgttctatggttgatcatcatatctcctaa------tgaaata---tttca-tgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
                                      |   |  |  |  ||  ||| |  | ||| ||||||  || |  |       || |||   || || ||   | |   || |  |  | | | ||          || ||||| |||||||| || || || |||||||| ||||||||||| || || || |||||||| || ||||||||||||||||| ||| | ||||||||||| |
gtaaccattttctaaacaatttgaaatggagtacgatatgcctttttttgcatccttccagtgctgaacatcatgactgcggaataactcgagataagcttgcactgaaaaactaaatgtctttgttaaaattggtgtgccttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCCCTGGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------tagttactggtaattgtt----ctatggttg---atcatcatatctcctaatgaaatatttca-tgttgatcctgatct-tatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
                                                       |  || ||   | || |       |||  ||   | ||  || |  |   |   ||  || || ||   | |   || | | | |||| |||     |  |  || ||||| |||||||| || || || |||||||| ||| ||||||| || || || |||||||| || ||||||||||||||||| ||| | ||||||||||| |
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 4
-tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
  |  |  |   || |  || |           ||| |   || |    | |  |    || ||  |    ||   ||  | | |   | ||||| ||||||||||||| || || || ||||||||||| ||||| |||||||| ||||| || |||||||| |||||||| ||||| ||||| |||||||||||||| |
gcatcttatcaaaactaatcaaacaccagctg-catgttggctgaatttacagctgtaattaatgattcctttggttttttctgttatccaatgactgcagGTTAACCAAATTGGTACAGTGACTGAATCTATTCAGGCTGCACTTGACTCAAAGGCTGCAGGTTGGGGTGTCATGGTTAGTCATCGGAGTGGTGAAACTG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 5
---tagttactggtaattgttctatggttgatcatcat-atctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
    |    |||  | ||      || || |  ||  |  |   || |    | |  |    || || ||    || | ||  | ||  ||    ||| |||||||||||||||| || || ||||| ||||| ||||| |||||||| ||||| || |||||||| |||||||| ||||| ||||| |||||||| || || |
aaacaccagctga-atttacagcttgctttaagatagttgttggctgaatttacagctgcaattaattcttcgtttgttttg-tgttgtcctt--tgactgcagGTTAACCAGATTGGTACAGTGACCGAATCTATTCAGGCTGCACTTGACTCAAAGGCTGCAGGTTGGGGTGTCATGGTTAGTCATCGGAGTGGCGAGACTG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 3
tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatct-taatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
 |   ||         ||  |   |   |||  |||  |  |     ||| |    |    ||       | || | |  | | |   | | ||| |||||||||||||||| || || ||||| ||||| ||||| |||||||| ||||| || |||||||| ||||||||  |||| ||||| |||||||| || || |
-aaacaccaactgaatttacagcttgcttcaagatagttgttggctgaatttacagttgcaattaatgcttcatttgttttgtgttgtccattgactgcagGTTAACCAGATTGGTACAGTGACCGAATCTATTCAGGCTGCACTTGACTCAAAGGCTGCAGGTTGGGGTGTAGTGGTTAGTCATCGGAGTGGCGAGACTG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------tagttactggtaattgttctatggttgatcatc-atatc-tcctaatgaaatatttcatgttg-atcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
                 ||  |  |  |   | |||||   |  ||  || | | | |  | |  |||       | ||| |     || | |  ||  |  | |  ||     |  |||||||||||||| || || || ||||| || |||||||| ||||| ||||| ||||||||||| |||||||||||||| |||||| ||||||| || ||||
gtaaaaataaaagtttttatattattttctcttttctaatctcaattctctagaccattttgacaaaacccccgttattggagaagaatttcaatttgtttgtaattcatggtttcacagGTTAACCAGATTGGGACAGTCACTGAGTCAATTCAAGCAGCACTTGACTCAAAAGCTGCAGGCTGGGGTGTGATGGTTAGTCACAGGAGTGGCGAGACAG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S83_55V6.1 (Physcomitrella patens), 3'ss of exon 3
-tagttactggtaattgttc-tatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
 ||  || |   | |  |||   ||| |  |   ||| |  | ||  |||  |    ||| || |   | ||| ||      | ||  |   |||  | ||||| ||||| || ||  | ||||| || || |||||||||||  | |||||||| || |  ||||||||||| |||||||||||||| ||||| ||||| |
gtatctaattacagtctttcacttggatcgtgcacatgtagcttag-gaatcaccgtatgatg-tttggttctcattcggtgaattttc---atgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ26490 (Selaginella moellendorffii), 3'ss of exon 5
tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaa-tgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
                         | | ||   | || |||      || | |||||   |||     ||| | ||  | ||| |      |  |||||||| || ||| | ||| |||||||||||||||| ||||| ||  | || || |||||||| ||||||||||| ||||| || ||| | ||||| || || |
------------------------gtaagcacggtgtcgccttccatcatttctcatgg-aatcgaatccttttttttttcttttctttcgctttttgcagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG

upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ26799 (Selaginella moellendorffii), 3'ss of exon 4
tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
         ||||      | | |     |||||| ||||   ||| ||||          |||||  | || |  |  | |||  |    |  |||||||| || ||| | ||| |||||||||||||||| ||||| ||  | || || |||||||| ||||||||||| ||||| || ||| | ||||| || || |
---------gtaagcacggtgtcgccttccatcatttctc---atggaatag--------aatccttttttttttcttttctttcgc----tttttgcagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
                            tcttaat  putative branch site (score: 3)
                      atcttatcttaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttactggtaattgttctatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- -ttactgg
- - - - - - - - - - -tggttga
- - - - - - - - - - - - - - - - - - -ctcctaa
- - - - - - - - - - - - - - - - - - - - - - tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacccaa