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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGAGGAAGCTTATGGATCCTGTGAAGGGATCCGACTACATGCCTACCTATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcccggactgcccctgaataaccctaattaacctaaattaatttttatttagtcaattaatcattccaaattttatttttcag

Basic information

species Vitis vinifera
transcript Vv09s0002g05160.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os06g39590.1 (Oryza sativa), 5'ss of exon 2
ATGAGAGGAAGCTTATGGATCCTGTGAAGGGATCCGACTACATGCCTACCTATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcccg-gactgcccctgaat-aaccctaattaacctaaattaatttttatttagtcaattaatcattccaaattttatttttcag
| |  |  |||||  | ||    || |  ||  |||| ||| |||| ||||| ||||||| ||| || || |||||||| ||||||||||| || ||||||||||   | || |    |  || ||| |   ||     |    |||| |     ||  | |  |  |     ||| |    |      |||
AGGGTACAAAGCTCGTCGACTTGGTCACCGGCGCCGAGTACGTGCCCACCTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCCTGGAAgtaagcaacgcgtgtacacatctcaatcagttcttgccgatt--aattcaccgaaatcaaatgcaaaatctgatccgatcaat-caacacag

upper sequence: Vv09s0002g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G004696_T01 (Zea mays), 5'ss of exon 3
ATGAGAGGAAGCTTATGGATCCTGTGAAGGGATCCGACTACATGCCTACCTATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcccggactgccc---ctgaataaccctaatta-acctaaattaatttttatttagtcaattaatcattccaaattttatttttcag------
| |||||||||||  ||||  | ||||| ||  | || ||| | || || || ||||||| |||||| || |||||||| ||||||||||| || ||||||| || | | | |  |   |   |||  | ||  | | ||    ||  |    || ||| |  |  | |    ||  |     |  ||| ||||      
ACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGGCGACGTCCCCTGGAAgtgagctcctctgcttcttcgttctgttttacttttactacgagtacgtggtcttatatattctttacttgatataactcgaatagtttctcagcgtatg

upper sequence: Vv09s0002g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G01550.6 (Glycine max), 5'ss of exon 2
ATGAGAGGAAGCTTATGGATCCTGTGAAGGGATCCGACTACATGCCTACCTATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcccgga-ctgcccctga---ataaccctaattaacctaaattaatttttattta-gtcaattaatcattccaaattttatttttcag--------------------------------------------------
|||||||||| || ||||||||||  || ||    || |||||||| |||||||||||||  ||||| || |||||| ||||||| || ||||| ||||||||||||      | ||     | |   || |       |     |  |||||||   |||   ||||||  | |||  | |||||||                                                         
ATGAGAGGAAACTGATGGATCCTGGAAATGGGATTGAATACATGCCCACCTATGAGGACAAAGATGGTGACTGGATGTTGGTCGGGGATGTACCCTGGAAgtaagttctatatatctattttttatttatgatttacgcttggaaaccttaatttcagttttcatcaattttttattttatattttatacaatgtatatattgtttcgttttcttaaaaaaaatttctcttggttctttttctag

upper sequence: Vv09s0002g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G01550.2 (Glycine max), 5'ss of exon 3
ATGAGAGGAAGCTTATGGATCCTGTGAAGGGATCCGACTACATGCCTACCTATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcccgga-ctgcccctga---ataaccctaattaacctaaattaatttttattta-gtcaattaatcattccaaattttatttttcag-----
|||||||||| || ||||||||||  || ||    || |||||||| |||||||||||||  ||||| || |||||| ||||||| || ||||| ||||||||||||      | ||     | |   || |       |     |  |||||||   |||   ||||||  | |||  | |||||||            
ATGAGAGGAAACTGATGGATCCTGGAAATGGGATTGAATACATGCCCACCTATGAGGACAAAGATGGTGACTGGATGTTGGTCGGGGATGTACCCTGGAAgtaagttctatatatctattttttatttatgatttacgcttggaaaccttaatttcagttttcatcaattttttattttatattttatacaatgtatata

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|110732015|gb|EE106932.1|EE106932
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|71884651|gb|DT033706.1|DT033706
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|71883956|gb|DT033011.1|DT033011
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110387049|gb|EC951689.1|EC951689
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110696702|gb|EE073060.1|EE073060
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110367267|gb|EC931194.1|EC931194
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110406887|gb|EC972474.1|EC972474
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|30125857|gb|CB911196.1|CB911196
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCA
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCA
EST: gi|110370124|gb|EC934304.1|EC934304
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|71887847|gb|DT036902.1|DT036902
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|30329031|gb|CD012293.1|CD012293
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110367289|gb|EC931218.1|EC931218
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110427195|gb|EC993628.1|EC993628
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110415971|gb|EC981916.1|EC981916
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|71860494|gb|DT009549.1|DT009549
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCT
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCT
EST: gi|110731059|gb|EE108847.1|EE108847
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|110396464|gb|EC962152.1|EC962152
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC
EST: gi|30136079|gb|CB921417.1|CB921417
EST:     TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAA                         AATGTTTGTGGAATCATGCAAGCGACTACGGCTAATGAAAAGCATTGAAGC
genomic: TATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcc ... tatttttcagAATGTTTGTGGAATCATGCAAGCGACTACGGCTGATGAAAAGCATTGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGAGGAAGCTTATGGATCCTGTGAAGGGATCCGACTACATGCCTACCTATGAGGACAGGGATGGAGATTGGATGCTGGTCGGCGACGTACCATGGAAgtaagtttcccggactgcccctgaataaccctaattaacctaaattaatttttatttagtcaattaatcattccaaattttatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA