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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttggtggggatgggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag

Basic information

species Vitis vinifera
transcript Vv12s0035g02180.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 5'ss of exon 4
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttggtggggatgggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag----
|| |||||||||||||| || || |||||||| ||||||||||| ||||| ||||||||||| || || || |||||||     || ||||| |||||||||     | ||   | |   | || |  |||||        | |  ||   |  ||||    ||  |  |    | || |  |      ||   | |||     
GGTTATCCATATGAAGAGATCCTCAGGACATTCCACAATCAAACAAGCATTATTATGTGCTCTTATCTTCCAATTTTCAAGTCTTTCAACAGGACAAAAGgt--ttgaccttgaactcactgaatcacacagtcacacattggtttgtgaac--agttagttacttaggccctgtttagttctccaaaaacttttcgcaaaaac

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G02160.1 (Glycine max), 5'ss of exon 4
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttg--gtggggatg---ggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag
||||||||||||||||||||| ||||||| ||||||||||| || |||||||| |||||||| || |||||  |||||||||||||||||||||| ||||||| |  || |  || |||   |||||| |     |   |  | ||    |  |  |||| ||     |  |  |  |   |  | ||||| |  |||       
GGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaac--agttcttacttca--aacctttccaccagacatcagaattcatgactttccaatttctgttctgatgcgaatgttggtattttgtgagcccag-----

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G13080.1 (Glycine max), 5'ss of exon 4
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttg--gtggggatg---ggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag
||||||||||||||||||||| | | ||| |||||||| || || |||||||| |||||||| || |||||  |||||||||||||||| ||||| ||||||| |  |  |  || |||   |||||| |     |   |  | ||    |  |  |||| ||  |  | ||  |  |   |  | ||||| | ||||       
GGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaac--aattcttacttca--aacctttccaccggacatcagaatttatgactttccaatttctattctaatgcaaatgttggtattttgtgcacccag-----

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA17G00710.1 (Glycine max), 5'ss of exon 2
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagttt--ggtggggatgggttgcc-----caagtttaacacaaaaac--ttaatgtaatgttttgggtaccccttgcag
|| ||||| |||||||||||| | || |||||||||||||| ||| ||||| | |||||||| ||||| || || ||||| |||||||| |||||||  ||||  | |  | | |  |    ||  |  |  |||  | |     |  |||         | | ||||  ||| |||  |||| | || ||| |      | |  |   
GGTTATCCCTATGAAGAAATTTTAAGCACATTTCACAATCAGACCGGCATAGTCATGTGCTCCTACCTCCCAATGTTCACCAGCTTTAATAGAACAAGGGgtaaacaaaattaaaaattaaaaatttccctatttccgattcttgttcgttatttcttataggattaagtcaacaactattaacg-aacgttgtattctgcaccag---

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G40090.1 (Glycine max), 5'ss of exon 2
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtc---------aaccttacagtttggtggggatgg-gttgcccaagt-ttaacacaaaaacttaat-gtaatgttttgggtaccccttgcag
|| | ||| |||||||| ||||| |  |||||||||||||| ||  ||||| | |||||||| ||||| || || ||||| |||||||| |||||||  ||||  | |  |    |||  |          || |      | |  ||   ||    ||  || | | ||   |   |    |||| | |||    | |    |     |||
GGTTTTCCCTATGAAGATATTCTAACCACATTTCACAATCAGACAGGCATAGTCATGTGCTCCTACCTCCCAATGTTCACCAGCTTTAATAGAACAAGGGgtaaacaatttttatttttatttttaaaaaaaatccctttttcttctgcacatcacattttccgattcttgttagttagttctaataggaataacgttgtattctgcaccag

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 5'ss of exon 4
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttc----gtcaaccttacagtttggtggggatgggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag
|| |||||||||||||||||||| ||||| || |||||||| ||||||||| | |||||||||||| | || |||||||  |  ||||||||||| || |||     | ||   |  |     |||  |||   |      |     || |  ||      ||    || | |  |||  | |  | || ||||     |||||
GGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttaccttccagctttaatgtctgcctctaataaaactccaactgtggggcttgttcttgtttcagatatctaaaatgaaatctttggtatg---tgcag

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|110715902|gb|EE094479.1|EE094479
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|33402286|gb|CF207913.1|CF207913
EST:     ATTATGTGCTCATA-CGATCCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: ATTATGTGCTCATACCTA-CCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|110703053|gb|EE079560.1|EE079560
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|110716453|gb|EE091450.1|EE091450
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|33409937|gb|CF215564.1|CF215564
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|110715796|gb|EE094253.1|EE094253
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|30298694|gb|CB975488.1|CB975488
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
EST: gi|33407421|gb|CF213048.1|CF213048
EST:     AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAG                         GAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG
genomic: AATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagc ... ccccttgcagGAGGCTTGATCCAATTAAACCATGGAAGGCCACAACCACTTCAATACATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttggtggggatgggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT