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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgttttggttgtttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT

Basic information

species Vitis vinifera
transcript Vv05s0020g03890.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g43684.1 (Oryza sativa), 3'ss of exon 2
aattgttttggttgtttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgtattatctctt---tga-atagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
   | | |   | || |  || |   |||    ||| | || ||      |   |   ||  || |  ||||| | ||| | | |||   |||   | | | ||| ||||||  |||| | ||    ||||||||| |||||||||||||||| || || ||||||   || |||||||||||||||   | |||||| || ||
--atctgtgcatagtatggtgctgtaattc-catttccatcattgcaaacttttcgttcaa-gtttgtactgagcttatcttttttaatgcttgattaatacagACATGGATAGCAAAATCAAGATGATGATCAAGATCATTGAAGAAGATGCTGAATCATTTGCAAAAAGAGCAGAAATGTACTACCGAAGGCGTCCTGAGCT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g28610.1 (Oryza sativa), 3'ss of exon 1
aattgttttggttgtttattgatcagattgattt-tttcctcttttttttttcaacagccact--gtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
   | || | ||||  | |   |  |||   |   | | | ||  | |  || | || | | |   ||  ||  | |        | || | |  |  || ||| ||||||   || || ||||| |||||||| ||  |  | |||||||| ||||| |||||||| || ||||| |||||||||||||| || ||||| ||
---ttttgtagttgaatttcagtttgatgcctgcatattcactcatatcatttagcaacaagtcaataaccaaggttgaagctaatcttgttttatgcaacagACATGGATTCAAAGGTTAAAGCTATGATCAAACTTCTCAATGAAGATGCTGATTCTTTTGCACGAAGAGCAGAGATGTACTACAAGAAACGCCCAGAGCT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
aattgttttggttg-tttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
|| | |  | ||   |||   |||   ||||    |        |   ||| |||  |        | ||   |     |  || || | |  | ||| ||| |||||    || || |||||||||||||| || ||  | |||||||| ||||| |||||| |||| ||||| |||||||||||||| |||||||| ||
aactatgctagtcaatttgaagatataattg-caatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
aattgttttggttgtttattgatc-agattgattttttcctcttttttttttcaacagccactgtattcactgatcctat-atgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
 ||| |  |     |  | ||||  | | | |     | |       |   |        | | | || | || |  ||| | || ||    ||||    ||| ||||||| |||||| ||||||||||||||||| |||||||| |||||||| || |||||| |||||||||| |||||||| |||||||| ||||||||
-attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatct-ttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G39070.1 (Glycine max), 3'ss of exon 1
aattgttttggt-tgtttat-tgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctat-atgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
  |  |     | |  | |  |  | | | | |     | |       |   |    ||  | | | ||   || |  ||| | || ||    ||||    ||| ||||||| |||||| ||||||||||||||||| |||||||| |||||||| || |||||| | |||||||| |||||||| |||||||| ||||||||
--tcatcaaaatatagtgacatatttacactaaaaaaattcataaaaatccatggttaggtaatct-ttaggtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGAAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G00910.1 (Glycine max), 3'ss of exon 1
aattgttttggttgtttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgat-cctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
 | ||  |      |    | |  | | |       | |   |  ||     ||       || ||| | |  |  | ||   | |  | | |||    ||| || |||  |||||| ||||||||||| ||||||||||| || || |||||||| |||||| ||||||||||||||||||| ||||||||||| || ||
taatgcgtcaaagatgctataactataatatacaagtgcgagtaattaaggaaatgagggttg-attgattcgtgtccatgcttctgttatgtttatgcagACATAGATACCAAAGTCAAAGCAATGATAAAGCTCATTGATGAGGAAGCAGATTCATTTGCAAGGAGGGCAGAAATGTACTATAAGAAGCGTCCGGAGCT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G44680.1 (Glycine max), 3'ss of exon 1
--aattgttttggt-tgtttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
   | | |    ||  |  || | |    | ||||  ||   ||   | | |    |  |  |||  || || | |    |    | |||| | | ||   ||| || |||  |||||| ||||||||||||||||| ||||| || || |||||||| |||||| ||||||||||||||||||| ||||||||||| || ||
tataatatacaagtgcgagtaattaaggaaatgatggttgattcgggtctatgcttat-gttacttaatccaataactgaagtgatgttatgtttatg--cagACATAGATACCAAAGTTAAAGCAATGATCAAGCTGATTGATGAGGAAGCAGATTCATTTGCAAGGAGGGCAGAAATGTACTATAAGAAGCGTCCGGAGCT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G22790.1 (Arabidopsis thaliana), 3'ss of exon 2
aattgttttggttgtttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgt----attatctctttga-atagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
                               ||| |  || | || |        |     | | |||  |  |  |||   |     |||| |  ||||  |||||||||||  ||||||||| |||||||| || ||||| ||||||||||||||||| |||||| | |||||||| ||||| |||||||| |||||||| ||
------------------------gtgcctctttctctctatgttctaaagtgttaagtgttttgttcctttgtattattgcttacggttattttcttgatgtagATATGGATTCCAAAGTGAAGGCAATGATTAAACTCATCGAAGAAGATGCAGATTCTTTTGCAAGAAGGGCAGAGATGTATTACAAGAAACGTCCAGAGCT

upper sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G14760.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------aattgttttggttgttta---ttg-atcagattgattttttcctcttttttttttcaacagccactgtattcactg------atcctatatgtattatctctttg------aatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
                                   || || ||  | || |   |||   ||   | ||  |||    || | | ||| || |     ||| |    ||      |   || | | | ||| | ||||      || ||| ||||||  |||||| ||  ||||||| |||||||| ||||  ||||||||||| |||||| | |||||||| ||||||| |||||| |||||||| ||
gtattctataatctttcttgacttctccttggtgttttttatgagtcttgaaaattgtggcattataatgcttttgatttgtatgtttaaagatattttgtttcttttggaagtcaatttaaaggaaatatttgtttgtgttgaaacagACATGGATTCCAAAGTCAAGACAATGATAAAGCTCATCGAAGCTGATGCAGATTCGTTTGCAAGAAGGGCAGACATGTACTTCAAGAAACGTCCAGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcaacagccactgtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT
                      cactgat  putative branch site (score: 3)
                                       ttatctcttt  putative PPT
                               tatatgtattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgttttggttgtttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - tggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gccactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatcc