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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA

Basic information

species Vitis vinifera
transcript Vv00s0357g00020.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatg-aaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
  | | |   | |      |   | |||   |     | |   |   ||  | || |    | |||     |  || |||  | |       |  |  ||||| ||||| |||||||||||  |||| ||| | || |||||| |||| || ||||| || |||||||||||||||||||| || |||||||||||||| |
-agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgg--gtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
 ||  ||  |   |   | | | |   | | ||   |  |   | | ||     | |     | ||    | ||   |   |  |  |   | |  || ||||||||||| |||||||| ||  |||||||| | |||||||||||||| || ||||| ||||| ||||| |||||||| || || |||||||| || || |
atgagaacatgcgtgctcgatcttaggtatttcc--tctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggat-acattacatgtgcctctagtaattgctgatgaaagtggttggtgggtc------cagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
       ||   | | |   |    ||  |    |||| | ||   | | ||   |    ||  |  ||||| |     |  ||    || |    |       ||||| ||||| |||||||||||  |||| ||||| |||||||||||||| || ||||| || || ||||| || || || || |||||||| |||||| |||
-------atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G055667_T01 (Zea mays), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggt-tggtgggt--ccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
   ||   || |  | |  ||  |    ||| | | |      |     | | |   ||     || |||  | |||   ||  |  |    ||  |   ||||||||||| ||||| || ||  | || ||| | || |||||||| || || ||||| ||||| ||||| ||||| || ||||| ||||||||||||||||
gcatttttttttcctgaagacattaaagctacctattgt---ctcaagcaaactttctggttgacttgtacgtactggacaattttttaccatgatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAGTGGGTGGATCTCGAGAGAACTTCTTTTTTGCGGGGATCGATAAAGTGAGGTTCCGGA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G24650.1 (Glycine max), 3'ss of exon 3
--ttgt-taaattc----tttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
  |||  ||| |||       | | |   || || |  | |  ||  ||   || |   |   || |   ||||    || ||| ||||  |   |  |   | |||||||| || || ||||| |||||||||||| | || |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||| | ||  |||
gattgcataagttccaacccatgaaagagcttttgcgttaagattgacagcagggtgtctgtaattt---tctaaaggtt-ctgttgaat-tatct--ttaatgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G07870.1 (Glycine max), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaag---ttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtg------ggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
        | ||  |||  | ||   |  |   |     || |  ||   ||  |  ||| |||||| || |  || || | |    || |   |       | | ||||||||||| |||||||| |||||||||||| | ||||||||| ||||||| |||||  | |||||||||||||| ||||| ||||||||| | ||  |||
-------ctgctgcttaagatccaactaatggaagagcttttgtgttaacattgacaacaggtgcctgtaat--tttctaaaggttctgttgaattatctctgatgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G19200.1 (Glycine max), 3'ss of exon 2
-ttgttaaattcttt---ttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
    |  ||| | |     ||    |  | |  | |    ||     |  | |  | || || ||| |  |       |      ||| |||   | | | ||||||||||| || ||||| || ||||| ||| | ||||||||||| |||||||||||||| || ||||||||||| ||||| ||||||||| |||| || |
aacctggaatgcatgaaagtaggggcgggatcttgtatgattt---ctctgttgtaata-atctgctttaaaagcggacatgaacaagaggtcttttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGCTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA

upper sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G05800.1 (Glycine max), 3'ss of exon 3
---ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
   || | |||  ||||        |   |  | |   ||  |  ||  | | || || || | | |  | |     |      | | |||   | | | ||||||||||| || ||||| || ||||| ||| | ||||||||||| ||||| |||||||| || ||||||||||| ||||| ||||||||| |||| || |
aacttctgaaagactttgagatgaacaactagtctt--gtatgatttctgttgcaata-atcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA

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|33404694|gb|CF210321.1|CF210321
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|30256504|gb|CB972347.1|CB972347
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|110387242|gb|EC951896.1|EC951896
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|26267567|gb|CA818630.1|CA818630
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|22011635|gb|BQ796669.1|BQ796669
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|110732593|gb|EE108014.1|EE108014
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|30256224|gb|CB972067.1|CB972067
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
EST: gi|34547229|gb|CF515461.1|CF515461
EST:     CTGGGCACTTCCCTGAGAGGCCAATTATCCCTGGTGTGCTCATGGTTGAG                         GCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC
genomic: CTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgct ... gtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA
                           tgctgat  putative branch site (score: 3)
                    tagtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA

- - - - - - - - acaaccc
- - - - - - - - - - - - - - ctatcaa
- - - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - ttacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg