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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcagaaggcttaagtgtgtttttaattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG

Basic information

species Vitis vinifera
transcript Vv18s0001g01020.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 13
gtaagattcagaaggcttaagtgtgtttttaattttctccattatattgctttaaggcctcctaaccgaccctgttgatt---tttcacctt-cagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
||||   |  | |  |       |   ||| ||||  |  |   ||| ||   ||   ||   |   || |   || ||    |||||  || ||||| ||||| || ||||| ||||| |||||||||||||| |||||||| || || |||||||| || ||||||||||||||||||
gtaaacatttggactcc-----atacatttgatttcatttaagctatggc---aaatacttacagtggagctcatttatgctgtttcatgttacagCTTTATGCCAACTATGCAATTGGGAAGGATGTCCAGGCCATGAAAGCCGTTGTGGGAGAGGAGGCGCTCTCTTCTGAGGATCTG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
gtaagattcagaaggcttaagtgtgtttttaattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
     |   |  | |  |   |  | |||     || ||    ||  || | ||||      | ||     ||  || ||| |    ||||||| ||||| || |||||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||| ||||||||||||
---gtacctattatgagtccataggctttg----ttttcagacatgatg-tgtaagatgaattgaca---tctactgttttctg---ttcagCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
---------gtaagattcagaaggctt----aagtgtgtttttaattttctccattatattgctttaaggcctc---ctaaccgac-cctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
          | ||     |     ||    ||| | ||   || | ||  | |   |   |   | | |         ||  |||  ||| ||  ||||| | ||||||| ||||| || || || |||||||||||||| ||||| ||||| || || || |||||||| |||||||| ||||||||||||
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctg--ttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
-----gtaagattcagaaggcttaagtgtgtttt-taattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
      ||    | |  |  ||||  ||  |    ||  |  |    | |||| |  |  |       |||  |||    ||   | || ||||||||||||| || |||||||| || ||||| ||||| || || ||||||||||| || ||||| ||||| || ||||| |||||||||
gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaa-----ttaattgacaacatt--ctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
--------gtaagattcagaaggcttaagtgtgtttttaattttctccatt--atattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
          |||  |   |   || |||||  |  |   | ||    | |    | ||  |   |  ||   | |  ||    |   |||  |     ||| | ||||| |||||||| |||||||||||||| || |||||||| ||||| || |||||||||||  | ||||| || ||||||
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcat--gtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
-----gtaagattcagaaggcttaagtgtgtttttaattttctccattatat-tgcttta---aggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
     |  ||  |||   |     |     ||    |||||    || |  | ||||| |   | | ||        | | || ||  |   ||  | ||| | || || || ||||| |||||||||||||| || || ||||| |||||||| ||||| |||||  | ||||| |||||||||
cacatgagagcatcatttgtggccatcaacttccccatttttctgatgaagtctgcttgagtcaagactttgggtttaacatggtgtctacccat-tgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
----------gtaagattcagaaggcttaa-gtgtgtttttaattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
          ||||  | |  ||   |||| ||    | || ||  |    | | | |  |  |  ||  |    |     |  || | |  ||||  | ||| | || || ||||||||||| || |||||||| || || ||||| |||||||| |||||||||||  | ||||| || ||||||
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataatta--actctgtgacaatggggagtttggatttgacaagtcgttgattcat-tgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG

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|110421686|gb|EC987986.1|EC987986
EST:     ACCATGCTGATGTGTCCAACCAG                         CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: ACCATGCTGATGTGTCCAACCAGgtaagattca ... tcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|37184152|gb|CF603506.1|CF603506
EST:     CCATTGGTGAGGGAATGACTCGTCGAGACCATGCTGATGTGTCCAACCAG                         CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACTCGTCGAGACCATGCTGATGTGTCCAACCAGgtaagattca ... tcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|30128132|gb|CB913471.1|CB913471
EST:     CCATTGGTGAGGGAATGACTCGTCGAGACCATGCTGATGTGTCCAACCAG                         CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACTCGTCGAGACCATGCTGATGTGTCCAACCAGgtaagattca ... tcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|110421897|gb|EC988201.1|EC988201
EST:     CCATTGGTGAGGGAATGACTCGTCGAGACCATGCTGATGTGTCCAACCAG                         CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACTCGTCGAGACCATGCTGATGTGTCCAACCAGgtaagattca ... tcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG
                                         tttttcaccttc  CT-rich tract
                                     ttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcagaaggcttaagtgtgtttttaattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT