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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag

Basic information

species Vitis vinifera
transcript Vv13s0064g00850.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
 |    || |||||||||||||||||    |||||||||||||||||||||||||||||||||||||||||||| |||| || |||||| | ||||||||||  | |  |    |  |     ||    | ||  |||     |   |  |   |||  |||  |  |  |  |||| | ||| |      |||||         ||           
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaatgctctcctttccctgtta--gattacgccaaattcta-gtttaaggttcgcatccgtgttgttagtattgcg----gttttatagtgagttt-----------

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgt-ttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
|     || |||||||||||||||||    || ||||||||||||||||||||||||||||||||||||||||| |||||||  ||  | | |||||||||| | | |    |    |||  | ||            | || |    ||| | | | || |||  | | |  |   |  ||  |    | | |     ||| |    | |        
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcccgaccgattttttgttg-----------ttttgttcgatctggtagtgttagtggatgttgattgattagtttgctcgcttaatcc---gaattgtagggtagg-----

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g59730.1 (Oryza sativa), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttc--tcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
|     ||    ||||||||||||||    || ||||||||||||||||||||||| ||||||||||||||||| ||||||| |||| | | |||||| |||   |  |  |||  |||| || | |  |||  || |   |||  || ||   ||    ||||   | | |    |||||| |    |  ||   || |||| |               
AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctctttgattcgtttcctagtcaccgctctagcttcattcgttcatcagtcaagcctggtacatatag----tgtgataaatcta--aatcatttggaattg--------------

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G050460_T02 (Zea mays), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttggga--aatacttgatgatggcag---
 |    || |||||||||||||||||    || |||||||||||||||||||||||||||||||||||||| || |||| || |||||| |  || |||                      | | | ||    || |  || | |  | |  |||   |   |    |  | | | |||||| ||| ||| ||  |   |    | | |   |||| | |   
TCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAG----------------------Tgtaaggaagctcacactttatattctgtctcatgcgtaaggctacttagctct-tgattaacgggttaggtagtcaaatcggtgcatatggatgtctgcct

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G044137_T02 (Zea mays), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttgg-tgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
|    ||| | |||||||||||||||    || ||||||||||||||||||||||| || |||||||||||||| |||||||  ||  | | |||||||||| |    | ||||| |||  |  |||| | | |   |   ||  | |||   |   | |  ||   ||| |   | ||    |  |  |  ||    |  |                 
AGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattccatttcttt--ttctaagcgttgccctttcctttccctctgatagaatcgaatgacattgagccgtatgcccgtatggatttgtacgagtga-----------------

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G027728_T01 (Zea mays), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttca-tattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
 |    || |||||||| ||||||||    || || |||||||| ||||||||||| ||||||||||||||||| |||| ||  ||||| | ||| ||| ||  || ||   |||    || || |    ||   ||  | ||||    | ||    ||   ||    |    || || | |  | | |||| | || || || |              
TCCACGGACAACATCAATAACAAGCTGCAGCTTGTTATGAAGAGTGGCAAGTACACTCTCGGCTACAAGACCGTCCTCAGGACTCTCAGGAACTCTAAGTgtaagtcatttctttcaagcaataatgtttgcggtagggcctttcgaagcatgtgaattca-tgcacat----ttggtaagtcgcagtttaattctttggcaaga--------------

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 5'ss of exon 2
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtt-tggggtttgtga---ttatcggattaagttttgggaaatacttgatgatggcag------------------------------------------
|| || || |||||||||  |   || || || ||||||||||| ||||||||||| || ||||||||||||   || |||| |||  |      |||||||  ||| | |  |     |  |       | || | |  || |||  |  |||      |    || ||   | ||||    | | |     | | |         ||  ||  |  |||                                           
ACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGGGCAAGGgtaagtt-tgcgctcgcgccg-acgcccgccgactggtgcttcctcaacccgcaccccctgccccttgtgccctgtgtggggctcagcaccgcacgctgccttctccaccagaaaactgcacatctatctcaccaactttgtctcctcttcttgcccaccgcag

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ14031 (Selaginella moellendorffii), 5'ss of exon 1
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
|| || || | |||||||||||   | || || |||||||||||||||||||||||||| ||||||||||| ||||||||    ||  | ||    || ||| ||  || | | ||| |     |    || |  ||||  ||  |   |||  |     |                                                         
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGCTACAAGACGGTGCTCAAATCGCTGCGCAGTGGAAAAGgtgtgaaatccctctttgtttctctt---gcgattgatccattggcgcattgggtgcgcag---------------------------------------------------------

upper sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ13021 (Selaginella moellendorffii), 5'ss of exon 1
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag
|| || || | |||||||||||   | || || |||||||||||||||||||||||||| || |||||||| ||||||||    ||  | ||    || ||| ||| | |     | ||  | |     || |  ||||   |  |   |||  |     |                                                         
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGGTACAAGACGGTGCTCAAATCGCTGCGGAGTGGAAAAGgtgtgtgaaat-ccctctttgtttctcttgcgattgatccagtggcgcattgggtgcgcag---------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|83276983|gb|DV940991.1|DV940991
EST:     GTACACGCTCGGTTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|30127653|gb|CB912992.1|CB912992
EST:     AGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: AGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|77588180|gb|DV223301.1|DV223301
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|71872071|gb|DT021126.1|DT021126
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|110376398|gb|EC941462.1|EC941462
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|37187884|gb|CF607235.1|CF607235
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|71867496|gb|DT016551.1|DT016551
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|71873230|gb|DT022285.1|DT022285
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|110733216|gb|EE109213.1|EE109213
EST:     GTACACGCTCGGCTACAAGACGGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|87585575|gb|DY474236.1|DY474236
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|110366148|gb|EC929857.1|EC929857
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|77579663|gb|DV218684.1|DV218684
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|77577312|gb|DV217370.1|DV217370
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|110378405|gb|EC943536.1|EC943536
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|71866692|gb|DT015747.1|DT015747
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
EST: gi|30137151|gb|CB922489.1|CB922489
EST:     GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGG                         GAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttata ... atgatggcagGAAAATTGATTCTGATTTCGAACAATTGTCCGCCGCTCCGAAAATCGGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC