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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattcatttttctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC

Basic information

species Vitis vinifera
transcript Vv07s0031g01860.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 5
-tatattcatttttctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgttcc-ctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
|| ||| | ||| || || |||| || | | |||| | | | | ||| || | | | || || | |||||||| ||||| |||| |||||| || || |||||||| ||||||||||| || || |||||||| || ||||| || |||||||| | || |
tggaggatatattttttataatc-tgt-tgttgccatgaccattactatttttatcgtggcagggcctaacattttctttttttcatctacctgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
---tatattcatttt--tctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
||| | || || ||| |||| ||| | || || | | | ||| | |||| || | ||||| || || || | ||||| | |||| ||||||||||| || || ||||| || ||||| ||||| || |||||||||||||| || || || || ||||| | || |
tatcatagcagtgcagacctgatgttcccttg-acttttacatattccttacat-gagcaaactgggactaatgctttcttcttcactcacttaatttcc---agTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G15280.2 (Glycine max), 3'ss of exon 5
tatattcatttttctcatattcatgcatgtttttgcatcctgct-cgtatcgtatcattta-ggaatgctgctgatgatttgccccactt-tgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
||| || | | || | | | | | | | || | | | | ||||| || | | | || | || || | |||||| |||||||||||||||| ||||| || || ||||| || ||||||||||| |||||||| ||||| || ||||| || || | |||||||| |||| |
--tataaatactgtata-gtttacctttactcaagaaaacaataatgaatactgtgactcctggaatactattattaaactgagctgctcctgctgtctgcagTTGTTCATCATTCTGTCTTGCACTATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGTAGGTTCACGGCTGTAACGTTCCAAGTCCTTGGTC

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G15250.1 (Glycine max), 3'ss of exon 4
---tatattcatttttctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
| ||| |||| | | | | | || |||| || | | | | | | | | | | | | | | | | | ||||| ||||||||||| | |||||||| || || ||||| || ||||||||||| |||||||| ||||| || ||||| || || || |||||||| |||| |
taatgaattttttttattttgaattccataagcattggcatttgcctaatgttgacttgtc-aatagtattattaa--actaatcttcttattctgtttgcagTTGTTCATCATTATCTCCTGCACCATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGCAGGTTCACAGCTGTATCTTTCCAAGTCCTTGGAC

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G31940.1 (Glycine max), 3'ss of exon 6
--tatattcatttttctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgt-tccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
|| | | | | | |||| ||| | || | || | | | | | | | || | ||| | | ||| | | ||||| ||||||||||| | || ||||| || || ||||| || ||||||||||| |||||||| ||||| || ||||| || || || |||||||| |||| |
gaaatcattttctattttgaattc-catatgcataggcctttgcctaatgtta-actttacaatagtacta-tattgaactaatctgcttcttctgtttgcagTTGTTCATCATTATCTCTTGCACCATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGCAGGTTCACGGCTGTATCTTTCCAAGTCCTTGGAC

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------tatattcatttttctcatattcatgcatgttt-ttgcatcct----gctcgt-atcgtatcatttagga---atgctgctgatgatttgccccactttgttccctg--cagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
| || | | | ||||| || | ||| || |||| || | | || | | ||| | | | | | | | | || || || ||| | ||| | || || || |||| || ||||| || ||||| |||||||||||||||||||||||||||||||| || ||||| |||||||| |||| |
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC

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|110714356|gb|EE091173.1|EE091173
EST:     GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATTCTGTCATGTACAATTGCGGTAGGAACCAACCTCAGCCAA
genomic: GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
EST: gi|34544353|gb|CF512585.1|CF512585
EST:     GGTTGACAAATAAAAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATT
genomic: GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATT
EST: gi|34546885|gb|CF515117.1|CF515117
EST:     GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
genomic: GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
EST: gi|22010955|gb|BQ795989.1|BQ795989
EST:     GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
genomic: GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
EST: gi|46918320|gb|CN547649.1|CN547649
EST:     GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
genomic: GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
EST: gi|71886650|gb|DT035705.1|DT035705
EST:     GTTGGACAAATAACAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATTCTGTCCTG
genomic: GTTG-ACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATTCTGTCCTG
EST: gi|22013082|gb|BQ798116.1|BQ798116
EST:     GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTG                         ATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA
genomic: GGTTGACAAATAAGAGAGTTGACAACTACCAATACAGTTTAATATCTGTGgtaagtattg ... ttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcgtatcatttaggaatgctgctgatgatttgccccactttgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC
                      tgctgat  putative branch site (score: 3)
 ccccactttgttccct  putative PPT
 tatcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatattcatttttctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - cctgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctg