Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaacttgatttctctttaagagagctctcctagagaattctgttatttcaaatttgagtctggtagccttcctttctatctaatctgtcaagaagattttttatttagaattcttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG

Basic information

species Vitis vinifera
transcript Vv11s0016g03070.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G35890.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtaagtcaacttgatttctctttaagagagctctcctagagaattctgttatttcaaatttgagtctggtagccttcct---ttctatctaatc--tgtcaa--gaagattttttatttagaattc--ttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                                                | |  | | | ||||   |        | | |||   ||| ||||  |   | | |  ||| |    | | |  ||  |   || ||  ||||   |||      || || ||  | |   |||    |  || ||| |    ||||  |||| |||||||| ||||||||| |||| ||||| ||||  ||  ||||||||||||||||||| |||||  | |||||||| ||||||||||| |||||||
gtcagtctcattctcctctcttttggatttctttattttttatagccaggatttgagcatgatggtttccagtttgtg-tctgacaga-aatttggagttataaggttttatggcgtttgtttttatatattttaagtaattcttgtttgcttaatatcttaaactggaaatgagatgaaacttggtgatttgatgtagGTTAATGATACCATTGGAACATTAGCTGGAGGCAGATTCTACAATCAGGATGTCGTTGCTGCTGTGATTCTTGGTACTGGGACAAATGCAGCATATGTAG

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G03730.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtaagtcaacttgatttctctttaagagagctctcctagagaattctgttatttcaaatttgagt-ctggtagccttcctttctatctaat--ctgtcaag-aagattttttatttagaattc---ttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                                                | |  | | | ||||   |        | | |||   ||| ||||  |   | | |  ||| |||  ||||     |   || ||  ||||   |||     |||  | || |  | ||| |    |  || ||| |    ||||  |||| |||||||| ||||||||| |||| ||||| ||||  ||  ||||||||||| ||||||| |||||  | |||||||| ||||||||||| |||||||
gtcagtctcactctcctctcttttggatttctttattttttatagccaggatttgagcatgatggtttccagtttgtg-tctgacaga-aatttggagttataaggttttagtgttggtttttatatattttaagtaattattgtttgctaagtatcttaaactggaaatgaaatgtaacttggtgatttgatgtagGTTAATGATACCATTGGAACATTAGCTGGAGGCAGATTCTACAATCAGGATGTCATTGCTGCTGTGATTCTTGGTACTGGGACAAATGCAGCATATGTAG

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G01070.1 (Glycine max), 3'ss of exon 4
------------------------------------gtaagtcaacttgatttctctttaagagagctctcc----tagagaattctgttatttcaaatt--tgagtctggtagcct---tcctttctatctaatctgtcaagaagattttttatttagaatt----cttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                                     |    |   ||  | |  |||| |||    | | |    |  | |   | |  | || | ||   ||||| | ||||  |   |  ||| | | | |  | ||  |   | ||  | | | |||          || ||| |    ||||  |||| ||||| ||| | |||||| ||||  |||  ||||      |||||||||| ||||||| ||||||  | |||||||||||||||||||| |||||||
gtcagtgctacttctcttcctgtttgtcttgttttctttttcccctttagtctggctttgagaataattttcagtttctatatggcggaaaatttagatcaatgagttttgtagtttcaattttttttcttttaaatttcctggttacttaatgtcttgaaccagagacaaaacttggtgatgtgatttagGTTAATGACACAGTCGGAACAGTAGCTAGAGCAAGATTCAGCAATCAGGATGTTGTTGCTGGAGTGATTGTTGGTACTGGAACAAATGCAGCTTATGTAG

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G01060.3 (Glycine max), 3'ss of exon 4
-----------------------gtaagtcaacttgatttctctttaagagagctctcctagagaa---ttctgtt---------------atttcaaatt-tgagtctggtagc-----cttcctttctatctaatct-----gtcaagaagattttttatttagaattc---ttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                        ||| |    ||  |||| |  |||       ||   |||  |   ||| |||               ||||||| |  ||||| | ||||       ||  |||   | |||  |     || |   |     || |  | ||          || ||| |    ||||  |||| ||||| ||| |||||||| | ||  |||  ||||      ||||||||||| |||||| ||||||  | |||||||| ||||||||||| |||||||
gtcagttccactttcctttctttataaattgttttcttttccccctaaagtctggctttgagaataattttcagtttgtatatggcagaaaatttcaattaatgagttttgtagtttcaatttttttttcttttaactttcttggttagttaaggccttaaactggagacaaaacctaacttggtgatgtgatgtagGTTAATGACACAGTTGGAACAGTGGCTAGAGCAAGATTCAGCAATCAGGATGTCATTGCTGGAGTGATTCTTGGTACTGGGACAAATGCAGCTTATGTAG

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G29130.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtcaacttgatttctctttaagagagctctcctagagaattctgttatttcaaatttgagtctggtagccttcctttctatctaatctgtcaagaagatt--ttttatttagaattcttcaatttgctctgc---tgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                                                                    ||    |  |||||    ||  || || ||   ||   |||| |   |  ||  |  ||||| | |     |  ||||||| ||||||||  ||||||||||||| || |||||||| ||| | | |||||| |||||||| || || || || ||||| ||||| ||||||||||| |
--------------------------------------------------------------------gtgagttctctttcgccttatgctctctagtgaatcccttttgtcatgtgtttgttgatttgtttttgacgttttacagGTTAATGATACCGTTGGAACACTAGCCGGTGGTAGATACTATAACCCGGATGTTGTTGCTGCTGTTATTTTAGGCACTGGGACAAACGCAGCCTATGTTG

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G19860.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtcaacttgatttctctttaagagagctctcctagagaattctgttatttcaaatttgagtctggtagccttcctttctatctaatctgtcaagaagattt-tttatttagaattcttcaatttgctctgctga---tacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                                               || | ||    | |           | ||  |        ||||  |       || |  ||  |||  |||||  |||    | ||   |   ||||||| |||||||| ||||||||||| || || ||||||||   | | | |||||||||||  ||||| || ||||| || || ||||||||||||||||| |
-----------------------------------------------gtgagttttcctctatacacacactcttttttcaactagcaatcaatttgtgtcatctacttgattatgattctctaatcccttttgtaaactttacagGTTAATGATACCATTGGAACACTTGCGGGTGGTAGATACACTAACCCGGATGTCGTTGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCG

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|110720179|gb|EE095876.1|EE095876
EST:     TAACGAAAGCCCTGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GGCAATGATACAATTGGAACCCTAGCAGGAAGTAAATATTATGATCAGGAT
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
EST: gi|161713800|gb|FC063788.1|FC063788
EST:     TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
EST: gi|161712030|gb|FC060046.1|FC060046
EST:     TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GTCAATGATACAATTGGAACACTAGCAGGACGTAGATATTATGATCA
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCA
EST: gi|110713107|gb|EE088738.1|EE088738
EST:     TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
EST: gi|294965564|gb|GW837163.1|GW837163
EST:     TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
EST: gi|110377656|gb|EC942735.1|EC942735
EST:     TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
EST: gi|110723174|gb|EE100188.1|EE100188
EST:     TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTG                         GTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT
genomic: TAACGAAAGCCATGGAAAGAATTGGTCTTGATATGCGCGTATCTGCTTTGgtaagtcaac ... gctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctgtcaagaagattttttatttagaattcttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG
                                            tgctgat  putative branch site (score: 3)
                                         ctctgct  CT-rich tract
           aagattttttatttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaacttgatttctctttaagagagctctcctagagaattctgttatttcaaatttgagtctggtagccttcctttctatctaatctgtcaagaagattttttatttagaattcttcaatttgctctgctgatacagGTCAATGATACAATTGGAACACTAGCAGGAGGTAGATATTATGATCAGGATGTCGTTGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG