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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGCGATTCGCGCTTTGGCGTCGGTGATTCGGTTCAGCCAGGCTACCACCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctttctaccgaaatgctggggaattccttgtttgtgttcgtagctgggcgtcaattttgtgtttttattcatctttattgataattgaaattc...

Basic information

species Vitis vinifera
transcript Vv09s0002g00390.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os12g31380.1 (Oryza sativa), 5'ss of exon 1
GGCCGCGATTCGCGCTTTGGCGTCGGTGATTCGGTTCAGCCAGGCTACCACCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctttctaccgaaatgctggggaattccttgtttgtgttcgtagctgggcgt-caattttgtgtttttatt--catctttattgataattgaaattc
||| || ||    ||  | ||  | || || || | ||||  ||| |||||||||||||| || ||||| |||||||||||||| |||||    || || || |   |   ||||  |     |   ||||   ||    | |||| ||   ||| |  |   || |||  ||  ||  |  ||       |      |  | 
GGCGGCCATCATGGCGCTCGCCGCCGTCATCCGCTCCAGCAGGGCCACCACCATGATGGAGCTCGAGATCGAGCTCAAGAAGGCATCCGACAAGCTCAAGgt-acccccacctactaaccgattatagaatg--ttaacagcgttcatacaagggtgcacggattcgtggattagttaccggctccgcaattttgcccacctt

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G084647_T02 (Zea mays), 5'ss of exon 1
GGCCGCGATTCGCGCTTTGGCGTCGGTGATTCGGTTCAGCCAGGCTACCACCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtg---ctttctaccgaaatgctggggaattcc-ttgtttgtgttcgtagc-tgggcgtcaattttgtgtttttattcatctttattgataattgaaattc
|||||| ||    ||| | ||  | || || || | ||||  ||| |||||||||||||| || ||||| |||||||||||||| || ||    || || ||   |    |   | |   |  |||| ||    ||  | |||   | | |  |     ||||  ||| | | ||| ||||  ||||| ||||| |         
GGCCGCCATCATGGCTCTCGCCGCCGTCATCCGCTCCAGCAGGGCCACCACCATGATGGAGCTCGAGATCGAGCTCAAGAAGGCATCTGACAAGCTCAAGgttgataacccggccgattcacctgctcggctgctctgtcgttcccgcttgctgtgctagcgtatattctatatttctattattctttgttgatcagcat-----

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G45180.1 (Glycine max), 5'ss of exon 1
GGCCGCGATTCGCGCTTTGGCGTCGGTGATTCGGTTCAGCCAGGCTACCACCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctttctaccgaaatgctggggaattccttgtttgtgttcgtagctgggcgtcaattttgtgtttttattcatctttattgataattgaaattc
 ||||| ||||||||  ||||  | || ||  | | |||||||||||||||||||||| | || || || |||||||||||||| ||||||||||| ||||| | || ||     | |    ||       ||| | | | | |   |  |||    |  ||| |   | || |||| | |  |                
CGCCGCCATTCGCGCCCTGGCCGCCGTCATAAGATCCAGCCAGGCTACCACCATGATGCAGCTCGAAATCGAGCTCAAGAAGGCCTCCGATTCTCTCAAAgt-attggtt-----caactctctct----ctccctctctctctctctctctgatgatttattct---tcttcattcctttgcag---------------

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 1
GGCCGCGATTCGCGCTTTGGCGTCGGTGATTCGGTTCAGCCAGGCTACCACCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctttctaccgaaatgctggggaattccttgtttgtgttcgtagctgggcgtcaattttgtgtttttattcatctttattgataattgaaattc
 ||||| ||||| ||  ||||  | || ||  ||| |||| ||||||||||||||||| | || |||||||||||||||||||| ||||||| ||| || ||     || | |       || |     |||| ||      | ||         |      | ||     || ||| || ||  |    |||| |    
CGCCGCCATTCGGGCCCTGGCCGCCGTCATAAGGTCCAGCAAGGCTACCACCATGATGCAGCTCGAGATTGAGCTCAAGAAGGCCTCCGATTTTCTCAAGgtattcactctat-------tgtttcttcattcatttccaacgctctctctctctctctctctctgacacattcttcttcattgctttgcattgcag---

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|349817979|gb|FQ407968.1|FQ407968
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351044484|gb|FQ443015.1|FQ443015
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|349807839|gb|FQ402230.1|FQ402230
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|349817476|gb|FQ407266.1|FQ407266
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCACG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351012185|gb|FQ426907.1|FQ426907
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|349814725|gb|FQ409948.1|FQ409948
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351024997|gb|FQ433414.1|FQ433414
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|349822671|gb|FQ412935.1|FQ412935
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351053555|gb|FQ459302.1|FQ459302
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351049282|gb|FQ429025.1|FQ429025
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|349821346|gb|FQ404478.1|FQ404478
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351048077|gb|FQ441249.1|FQ441249
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351031133|gb|FQ444960.1|FQ444960
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|351056004|gb|FQ453465.1|FQ453465
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|352790509|gb|FQ478149.1|FQ478149
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|294966190|gb|GW839413.1|GW839413
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGGTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|349822083|gb|FQ408412.1|FQ408412
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|161715268|gb|FC068022.1|FC068022
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
EST: gi|110392389|gb|EC957773.1|EC957773
EST:     CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAA                         TCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG
genomic: CCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctt ... tgcatttcagTCATGGGACACAACCTCCATCTCTTTGACGGCTGGCTGCGATCTGTTCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCGCGATTCGCGCTTTGGCGTCGGTGATTCGGTTCAGCCAGGCTACCACCATGATGGAACTGGAGATTGAGCTCAAGAAGGCTTCCGATTCTCTTAAAgtgagtgctttctaccgaaatgctggggaattccttgtttgtgttcgtagctgggcgtcaattttgtgtttttattcatctttattgataattgaaattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgaaa