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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA

Basic information

species Vitis vinifera
transcript Vv03s0063g02450.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 4
gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactg-gtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
      ||| |   ||||    |||||  |||| |      |    | |    |    |||  | || | |  |  || |     ||||||| || ||||| |||||  | |||||||||||||||||||||||||||||||||||||| ||||| ||  | ||||| || || || |  ||   ||
-----gttggtgaatgtt--gattgttactttgcagttctctgcagtctatggatctttgaaagtgtctgtgttacatttgttgcagGTTATCATCGTGACCAGCTCGTTGATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCTAATGCAATAAGAGTTCTTTGCCGCATCATTGACTCAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
gttaaattgattgttg--ttttatttgtttgtttgt--accaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
|||    ||| | |||  || || |   | |||||   |  ||  |    |||| |||   ||   |  ||| | || | |       |||| || || || || |||||  | |||||||||||||||||||| ||||||||||| || |||||||||||| | ||||| ||||| || |  ||   ||
gttgg--tgactattggtttctactatgtggtttggcaaataatgtggaatgtggaaatgact--ttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
gttaaattgat--tgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttata--tacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
|||||||  ||  |||| |   ||   |    |  |    |     | |     || |      ||||| |   |||||   |  || |||| || || || || |||||| | ||||||||||||||||||||||| |||||||| || || ||||||||| | ||||| ||| ||||||  ||||| |
gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttga-gctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 4
----gttaa-attgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
    || || |||| ||| |  | | |  ||| |     |  ||  |    ||||   |   ||  |   ||| | || |||       |||| || || || || |||||  | |||||||||||||||||||| || |||||||| || ||||| |||||| | ||||| ||||| || |  ||   ||
gttggtgaacattggttgctactatgtg-gttcggca--aataatgtggaatgtggggatgacttcc--atttgtgatctattgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACCGATATGTACCGTGCAAACGCTATTAGAGTTCTTTGTCGTATTATCGACTCAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 4
-----------------gttaaattgattgtt-gttttat-----ttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
                  ||  ||     ||  | || |      |||| ||| | |  |||    |  |    |  || ||  ||  |||||  |   | |  |  ||||||| || || || ||||| || ||||||||||||||||| ||||||||||||||  | || ||||||||||| || || ||||| || ||||||||||
gttacaaattcttgcaattttcatgagcagtcagattcacgaatattgtctgtatatcacaaacagagattctgaccgttctatctcttttattttacttttttaccagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACGGATGGAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 4
---------gttaaattgattgttgttttatt---tgtttgtttgtaccaacttt-atttgtgaaa--------agtgctgactggtttataattt--atatacaaa-agGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
           | |    | | || |||||||   | ||  | ||||    || | || ||||  |          |  | | |  | |||   ||  || |  ||| ||||||| || || || ||||| || |||||||||||||| ||||||| ||||||||| ||||||||||| ||||| || || ||||| || || || ||||
gtttcattttcttatgcaacttttattttattttatattcttgtgtatggtctgtgatctgtgttactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGACATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
gttaaattgattgttgttttatttg-tttgtttgtaccaactttat-ttgtgaaaagtg---ctgactggtttataatttata---------tacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
|||| |     |  ||     |  | ||  |   ||    || ||| ||   || || |   ||||||| | |||   || ||         |  || ||||||| || || || ||||| || ||||||||||||||||| ||||||||||||||  | || ||||||||||| || || ||||| || || |||||||
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 4
-------------------------------gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
                                ||| ||| ||   | |  ||| || |  ||  ||| |||||   || | || | | ||  ||    | |||||| ||   || ||||||| || || || ||||| || |||||||| ||||| ||||||| ||||||||| ||||||||||| ||||| || || ||||| || || || ||||
gtttcattttcttatgcaacttttcttttattttagattcatgcgtatggtatgtgatctttattactaacttggattataaatatt-ctatct---ctttaattttta---aatagGTTATCATCGTCACAAGCTCTCTCATGAAGGATATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
----gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatataca-aaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
    || || || | |    ||  ||  |    |  ||  ||  | |  | |  | |  | ||||   |||  |  ||| |   |  | ||||||| || || || ||||| || |||||||| |||||||| || | |||||||||||||||||||||||| || || ||||| || ||||  || ||||
gtctgtaaattttactcaatttcaatacgaacatc-gtcgcacttattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA

upper sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
                    | ||  |  |   ||   | | | ||   |  |  ||  |  | |   | |   |  ||||  ||  ||   | ||  |     |||||||||||| || |||||| | |||||||| ||||| |||||||| ||| | ||||| || || ||||| ||||| |||||  |||| || |||||  
tgcattgtgccaagatcttatcaacattttgcatgcactgtattttctatactttcagttacagtcacgtattatattgacgagtgcatctctgatgca-----gGTTATTATTGTAACAAGCTCATTAATGAAGGATATGAACAGCAAGACAGATCTTTATCGCGCGAACGCTATACGGGTCCTCTGCAGAATCACAGATGGTG

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|294964857|gb|GW838660.1|GW838660
EST:     GGAGAATGGTGTATTTAATGATAAAGGAGCTTTCTCCTTCTGCTGATGAG                         GTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGAT
genomic: GGAGAATGGTGTATTTAATGATAAAGGAGCTTTCTCCTTCTGCTGATGAGgttaaattga ... tatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA
                        tgctgac  putative branch site (score: 2)
                               tggtttataatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA