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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaacaatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA

Basic information

species Vitis vinifera
transcript Vv13s0147g00220.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 4
aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaa-caatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
  |  || |||      | |||  |  | || ||   |  |   |  | ||| ||||| | |  | | |  | | |    |  |     ||  ||||    |  ||| ||||| ||||| || |||||||||||||| || ||||| || || ||||||||||||||| |  |||| ||||| 
--tgattccatctaaatactatagtgttaca-ttaaccgctgcataatttttatttggat-tagttaacagtaatattttcccttcccttttgtatgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G109785_T01 (Zea mays), 3'ss of exon 4
aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaa-caatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
  |  || |||      | |||  |  | || ||   |  |   |  | ||| ||||| | |  | | |  | | |    |  |     ||  ||||    |  ||| ||||| ||||| || |||||||||||||| || ||||| || || ||||||||||||||| |  |||| ||||| 
--tgattccatctaaatactatagtgttaca-ttaaccgctgcatagtttttatttggat-tagttaacagtaatattttcccttcccttttgtatgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G066496_T01 (Zea mays), 3'ss of exon 4
aatatttgcatt-agttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaacaatgttga-------ttaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
         ||| |||  |  | |||        | |  | |||         ||||       || |    |||||  |  || |          ||   |||    |   || ||||| ||||| ||||||||||||||||| || || || || || ||||||||||||||  |  |||||||||| 
--------tattgagtctaaaacttttg---gactctagagtctcctgcagaatttttatcaagattagttcttacagtaatatttccccctcccttttgcatgtatctagCGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCT

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G42580.4 (Glycine max), 3'ss of exon 4
-----aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaacaatgt--tgattaatatgctagTGA---TGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
     || | |  ||    || | ||||     ||   |||    | ||  ||| ||  || |    | | |  ||||||| |   || |  || | |   ||  || ||   ||| |||||||||||||||||||| ||||||||||||||||||||||| || || ||||| || ||||| |||||||| 
gaaataaaaatctcaccgattgattattg----cctaatgt---gttttcactgcttcattagagccttttagtctttacagatttatttgatgttcatattgtcagAGACACTGGGCGCAAAGTTGAAGATCCTGATATGTTAGAGAGAATTCGACTTACCATTATTAACAATCTGTTGAAATATCATCCT

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G24450.4 (Glycine max), 3'ss of exon 4
-----aatatttgcattagttaagtatt-ttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaacaatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
     || | |  || |  | |  |||| |  |    ||| |||| |  ||| |       | ||| ||  ||   ||||    |   |  | |||   |         |||||||||||||||||||||||| ||||||||||| ||||| ||||| || || ||||| || ||||| |||||||| 
gaaataaaaatctcactgatcatttattgtctaatttgtt-ttcactgcttcattagagccttggtctttacaga-tttatttgatgttcat-attgtcacagAGACACTGGACGCAAAGTTGAAGATCCTGATATGTTAGAGAGGATTCGGCTTACCATTATTAACAATCTGTTGAAATATCATCCT

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ26563 (Selaginella moellendorffii), 3'ss of exon 2
aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaacaatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
                                      ||    |   |    | |    |  |   || | || ||   ||||      | | |     |  ||||||||| ||||||||||| ||  | || ||    || ||  | |||||||||| |||||||||| |||||||||||
------------------------------------gtaagtgcttacgcccctctatacgacaaggtcttctaaaaggaaatg------actgtagAGCTACTGGACGCAAGGTTGAAGATCCCGAGCTTTTGGAATCGATCCGCTTGACAATCATCAGCAACCTTTTGCAGTATCATCCA

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|22014312|gb|BQ799346.1|BQ799346
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|110392201|gb|EC957452.1|EC957452
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|110359925|gb|EC922269.1|EC922269
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|22014843|gb|BQ799877.1|BQ799877
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|22014313|gb|BQ799347.1|BQ799347
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|22014315|gb|BQ799349.1|BQ799349
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|22013161|gb|BQ798180.1|BQ798180
EST:     TCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: TCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|110430431|gb|EC996990.1|EC996990
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|110394001|gb|EC958326.1|EC958326
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
EST: gi|110358677|gb|EC923071.1|EC923071
EST:     GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAAT                         TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC
genomic: GTTACGACTGAGGGATCAGTCACTCAAACAAAATTTTTCATTACCCGAATgtaagtgttt ... aatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtttttttgggtgttatcatcctttacaaaacaatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
                                         gattaat  putative branch site (score: 3)
                                   aatgttgattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaacaatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - ccagttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa