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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatg-gtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                                            |  |   |||   || | |  ||| ||     ||     || |  | | | ||| |  |    |  || || |  || |  | ||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| | |||||| |  | || ||||||||||||||||  || 
---------------------------------------------------------------------------gtacatgtacatcctgtttgctgtt-atgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatg-gtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG------
                                                                            |  |   |||   || | |  ||| ||     ||     || |  | | | ||| |  |    |  || || |  || |  | ||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| | |||||| |  | || ||||||||||||||||  ||       
---------------------------------------------------------------------------gtacatgtacatcctgtttgctgtt-atgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagt-ttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                              |   ||| |   ||| ||   |   |    |  |   | | ||    |  | |   || ||||  | ||    ||| | |  |        ||||  ||||||||| || || ||||| ||  | |||||||||||||||||||||||||| ||| | || ||  || | || |||| ||| |||||| | |||
-------------------------------------------------------------gtaggcttctgcaattgaatgcatcttgccctactcagtaacat----cttgtatcggacattgtatgttgacaattggtcctttg------ctgt-acagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                        ||    ||   |  | | ||| ||       | ||||| | |||  | |||       || | |   | |  ||    ||| | | |||             |||||  || ||||||||||||||  ||||||| ||||| || ||||| ||||| || ||||| ||| |  | ||||||||||| |||||||  || 
-------------------------------------------------------gtaagtcttgtttgctgtgattaaatccttgttctggtgct-gttcctttga------gagctaaacattatcttctgtattcggcactg-------------cagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G443953_T02 (Zea mays), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagt-ttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                   |   | | |  |   ||| |   ||| ||   |   |    |  |   | | ||    |  | |   || ||||  | ||    ||| | |  |        ||||  ||||||||| || || ||||| ||  | |||||||||||||||||||||||||| ||| | || ||  || | || |||| ||| |||||| | |||
---------------------------------------------------tggttgataggtaggcttctgcaattgaatgcatcttgccctactcagtaacat----cttgtatcggacattgtatgttgacaattggtcctttg------ctgt-acagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagat-tgagtttactgattagactctgatatg-gtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                                                  |  ||| | ||      | ||   | ||  |   | | | | |   |||    | || ||  |    || || |  |||||||| || |||||||||||||| ||| |||| || || || ||||| ||||| || ||||||||| |  | ||||||||| | ||||| |  || 
----------------------------------------------------------------------------------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagTAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATAGTGGCAATTTGGAGAGACGACCTGAGTAAA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                     | |  |  |||   | |  ||     ||| | || | | |  ||| | |  | || ||  |       |     ||   ||   ||  |||||   |||    ||  | |||| | | | |||| |||||||| || || |||||||||||||| ||||| || || |||||||||||  |||||||| |  | ||||||||||| || ||||  |||
-----------------------------------gtattattt-taccgttgtgatattttattaatgatattactgtacaaagagaaaggggggggg------ggggggggtgattagaatgcagttt---gatgtagctgagttatgcttt-tggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                             || || | || |     |   ||| | | | | |    ||  ||  | |  ||     | ||    |    ||   ||  |||||   |||    ||  | |||| | | | |||| |||||||| || || |||||||||||||| ||||| || || |||||||||||  |||||||| |  | ||||||||||| || ||||  |||
--------------------------------------------gtattattctactgt-tgtgatcttttattaatgacatcactgtacagagagaga----aagagagggttgattagaatgcagttt---gatgtagctgagttatgcttt-tggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                ||||||  || |  |   ||  |||| ||   | |||| ||   || |||     ||     || || ||   ||  |||||||   |    ||    ||||  || |||||| ||||| || || || || ||||||||||| |||||||| || ||||| |||||  |||||||| |  | ||||||||||| |||||||| |||
-----------------------------------------------gtaattttctaaagttgggctgttttccttc--ctgacattac--tgatagggaggattgattagaaatttagaatgcagtttacatttatagctgaagtatg-ccttttgcagCAATCGAATTCCAGAGGCAGCTTTAATGGCTCGATCTTATCTCCCAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                |||| |  || |  | | ||  || | ||||   |||| ||   || |||     | ||   |  |   ||   ||   |||| |  ||  | | ||       || |||||| ||||| || || || || ||||||||||| |||||||| || ||||| |||||  |||||||| |  | ||||||||||| |||||||| |||
-----------------------------------------------gtaatcttctaaagttgtgctc-ttccctttat--gacattac--tgatagg--gaaggattgattagaatgcagttacattta-tagttgaagtatg------ccttttgcagCAATCGAATTCCGGAGGCAGCTTTAATGGCTCGATCTTATCTCCCAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                                    |||||||||  || |   |  |||  ||   ||  |  |  ||   |  ||   ||   | |  | || | |    || ||  ||| |  |||||| |||||||| ||||||||| | |||||||| ||||| ||||||||||| ||| | |||||| |  |  | |||||  | || |||| ||||
-------------------------------------------------------------------gtatttcatt--actgttcacttggccgt---ttggaaaaatcaaatatgtgtcttttgttatctttatgacaa---gaaattatct-tgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 24
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                                    ||  |  ||||  |     ||     || |   ||||   || | || |    |||  || || || |  ||   | |||||||    | ||||||||| ||||||||||| ||| | |||||  |||| |||||||||||||||||  | || ||| |  |  | |||||||| ||  | | ||||
-------------------------------------------------------------------gtacattgtttactatttcttacat--gtggaacatatattcccgcaact---aattacgtcta-tgct--gatattaatatggt----tacagTAATCGAATACCTGAAGCCGCTCTGATGGCGAGATCGTACCTTCCAAGCAAGGTCTCCGAAATAGTGGCATTGTGGAGAAACGATTTGACCAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
                                                                    || |||||| |  || || |    ||  |||||  |  | | |     |  |  ||  ||| ||||  |        ||||  | |  | |||||| |||||||| ||||||||| | ||||||||||| || ||||| ||||| ||| | |||||| |  |  ||||||| || || |||| ||||
-------------------------------------------------------------------gtaattcatt-agtagtcact----tgagagtttggaaaatcaaatttatgcacctttggttaactgtgtga----caatattttttcct-cagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA