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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA

Basic information

species Vitis vinifera
transcript Vv06s0080g01110.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
--------gtgctattttatatctaacgcaatatatcctgtggcataac---atcctgtcaa-ttgaaacgtttccat----tatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
         | ||  | | | | |  |  |   | |    |  ||   |   ||  ||||||  | | | || |  |     | |  |||||||| || ||||||||||||||||| || |||||||||||||| || || || || || |||||| | ||||| |  || |  |||||
gttaatatttccttctgtttttttctcatatcctgtttgctaacacgcctttattttgtcaagcttatatgtatgtaaaatgttttgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC214168.3_FGT001 (Zea mays), 3'ss of exon 3
----------------gtgctattttatat-ctaacgcaatatatcctgtggcat-------aacatcctgtcaattgaaacgtttccatta--tcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
                    |   | || | ||||  |   || ||   | |  |         | | |||  |  |  | |||  | || |   | ||||| |  ||||||||||| |||||||| ||||||||||||||||| |||||| | ||  | |||||||||||||| |||||    |||||
atgttaggtgtatgtaacttttcctcatttactaagccggcatttctctttgtttctcttgagtcttgctgcaagcttcagcgtgactatgaaaactcagGTTCGTAAGAGGCGTATGTATGACATTACAAATGTCCTTGAAGGGATTGGTTTGATAAAAAAGAAGTTGAAGAACAGAATATGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 6
------------------------gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaa---acgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
                         || |  |||   | |    |  |  |||| ||         |  ||| ||    |   |  | |   || |  ||||||||||| ||||||||||||||||| || ||||| |||||||| || || || || || |||||| | ||||| |  || |  |||||
gatgatattgatgttgactagaggttggtgctttccttttggtaccttg-atccagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G052515_T01 (Zea mays), 3'ss of exon 4
-gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaa-acgtttcca---ttatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
  || |  |||   | |    |  |  ||||  |         |  ||| ||    |  | |||  |   || |  ||||||||||| ||||||||||||||||| || ||||| |||||||| || || || || || || ||| | ||||| |  || |  |||||
gttggtgctttccttttggtaccttg-atccaatcatggtttcttttgttaaacatatgcatttataactttttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAAAAGCTTAAGAACAACATCCGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 6
--------------------------gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattg-aaacgtttcca-ttatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
                           || |  |||   | |    |  |  |||| ||         |  ||| ||    |  ||| |  |  | |  ||||||||||| ||||||||||||||||| || ||||| |||||||| || || || || || |||||| | ||||| |  || |  |||||
cagatgatattgatgttgactagaggttggtgctttccttttggtac--ttgatccagtcatggtttcttttgttaaacatatgcgtatatagctttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G041701_T01 (Zea mays), 3'ss of exon 4
----------------gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
                 |   | ||   ||||      ||  |  |  | |    | |     |||     ||  || | |  ||  ||||| || ||| |||| ||||||||||| || |||||||||||||| ||||| || || |||||||   | ||||||||||| |  |||||
gttacagatgttttcattttcagttgtcatctcttttcattcactcaatagt-cgatacatattca--cagaattttcctacaatt-cagGTTCAAAAGCGGCGCATATATGACATTACCAATGTCCTTGAAGGCATTGGACTAATAGAGAAGACACTTAAGAATAGAATCCGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
---------------------------gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA-----------
                           ||||| |  | |   || |   ||  |  |  |||  |    |  |    ||    |  | |   || |  |||||| |||| ||||||||||||||||| || ||||| |||||||| || || |      |       |  | | |||| | | |  | ||           
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtc-atggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC233850.1_FGT005 (Zea mays), 3'ss of exon 4
-----gtgctatttt-atatctaac-gcaatatatcct--gtggcataacatcc--tgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
         | |||  || |  ||| |  || | |  |      | |   |  |  |    ||| | || |||||   |   ||||| || ||| | || ||||||||||| || |||||||||||||| ||||| || || |||||||   | ||||||||||| |  |||||
gttacagattgtttccattttcaactgtcatctcttttcatccacttggtagtcgatacatattcagacttttcctacaattcagGTTCAAAAGCGACGCATATATGACATTACTAATGTCCTTGAAGGCATTGGACTAATAGAGAAGACACTTAAGAATAGAATCCGTTGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
-gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
  |  |||  | |      | |||   || |  ||   |||  |  | | | ||    | ||||  |   | ||||| || |||||| | |||||||| ||||||||||| |||||||| ||||| || || || |||||  | || ||| ||||||| |||||
gttaatataatttcatctgctcaaatgattccatgctgtaaagttttattatttt---cttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA

upper sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
-gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccatt----atc-acagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
  |  |||  | |      | |||   || |   |   |||  |    | | ||||    ||||  ||    |||  ||||| || |||||| | |||||||| ||||||||||| |||||||| ||||| || || || |||||  | |||||  ||||||| |||||
gtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
               gcataac  putative branch site (score: 3)
                                        tttccatt  putative PPT
                              aattgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA