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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaactcatactattgagtcataattctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------caaactcatacta-ttgagtcataattctcataaaaatagttagaagtgtcaca-atatggt--ttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
|| || | || ||| | | || || |||| ||| | | | | ||| ||| | || | | | || |||| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| | | | ||
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
caaactcatactattgagtcataatt-ctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
| ||| | | |||||| || | | | | | | | | | | || | | | | || ||||||| || ||||||||||| ||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||
-ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------------------------caaactcatactattgagtcataattctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctga----acagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
|| || | ||| | |||||| |||| || | || | || | || || ||| || || ||||| | | |||||||| ||||||||||| ||||||||||| ||||||||| | ||||| |||||||||||||||||| |||| || || ||
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataagatc-tgctactagacaataatt-tcatgtgcttaagtttcagcacactaccata-catggttaatgatttca-attgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------caaactcata----ctattgagtcataattctcataaaaatagttagaagtgtcacaatatg-----gtttatttgatcattgtgtatgagaaattttttcctgaac-----------agGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
|| | || ||| | | |||||| || | | ||| | ||| || ||| | | || | | || | | || | | || ||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| || ||
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatt-tctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 3
caaactcatactattgagtcataattctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgag-aaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
||| | | | | | | || | | | | || || ||| || | ||| | || |||| ||| | ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||||||||||||||| || |||||
-aaagttacatagaaaaattaattttgcttttgccgtcttgtattgcttcgaaaaatgaatttctacatcttgtcacatagttgaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
caaactcatactattgagtcataattctcataaaaatagttagaagtg--tcacaatatggtttatttgatcattgtgtat-gagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
| |||| | |||||| | | | ||| | || || || ||| | | || | || | |||| ||| | ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||||||||||||||| || |||||
---aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 3
caaactcatactattgagtcataattctcataaaaatagttagaagtgtcacaatatggtttatt-tgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
|||| || | | |||||| | ||| ||| | | || || |||||| ||||| ||||| || || ||||||||||| |||||| ||||||| || |||||| ||||||| || || ||| ||
-------------------------------------------gtatgtctcattct--tttattgttcctgttgctgatgcggtgcgtgtttct--acagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ10709 (Selaginella moellendorffii), 3'ss of exon 3
caaactcatactattgagtcataattctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
| || ||| | | || | | || | | | ||| | |||||| ||||| ||||| || || ||||||||||| |||||| ||||||| || |||||| ||||||| || || ||| ||
-----------------------------------------gtatgtctcattcttttattgttcctgttgctg-atgcggtgcgtgtttgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG

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|156738161|gb|EV242282.1|EV242282
EST:     CTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAG                         GATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTA
genomic: CTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAGgtacatccat ... tcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTA
EST: gi|110696169|gb|EE075018.1|EE075018
EST:     CTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAA                         GATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTA
genomic: CTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAGgtacatccat ... tcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTA
EST: gi|30302057|gb|CB978851.1|CB978851
EST:     CTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAG                         GATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTA
genomic: CTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAGgtacatccat ... tcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG
                 atttgat  putative branch site (score: 5)
 ttttttcct  putative PPT
 tatgagaaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaactcatactattgagtcataattctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
caaactc
- - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - -cacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaatt