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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttttcatgttcatcagtgttctttatgatgcactacttcaatttcctgaacaattaatcaattgttatcttagaaattaaaaaaaaaaaggagagagaaataactatttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAG

Basic information

species Vitis vinifera
transcript Vv02s0025g04840.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g04840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
gtaggtttttcatgttcatcagtgttctttatgatgcactacttcaatttcctgaacaattaatcaattgttatcttagaaattaaaaaaaaaaaggagagagaaataactatttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAG
                                                    |  |    |  |   ||| | | ||      |  ||  | |    | |     ||    || | |  ||| || || | ||  | | |||               || |||||||  ||||| |||||||| |    ||| ||||||||||| ||||||||||||||  |||||| |||||||||| |||| || |||| |||||||
---------------------------------------------------gtagatg-ctggtgccttgctgtttttttttatttaattatattttataactggattttcatgttatggctattgttatgttggatattct--------------tatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG

upper sequence: Vv02s0025g04840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4
gtaggtttttcatgttcatcagtgttctttatgatgcactacttcaatttcctgaacaattaatcaattgttatcttagaaattaaaaaaaaaaaggagagagaaataactatttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAG
                                                    |  |||  |  |   ||||  | ||     || | |||  | |           |   ||  |  ||  |  | || |         | ||      | || |  || | |||||  ||||| |||||||| |     || ||||||||||| ||||||||||||||  |||||| |||||||||| |||| || ||||  ||||||
---------------------------------------------------gtagaca-ctggtgccttgtgttttttttttttgagaaattata-----------tttttaactggattttcattttatggctattcttatgttggttattctt--atttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG
















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|294964687|gb|GW838490.1|GW838490
EST:     TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG                         GTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGC
genomic: TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAGgtaggttttt ... catgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGC
EST: gi|26258628|gb|CA809691.1|CA809691
EST:     TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG                         GTTAGGGTCCCTGTTGGAAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
genomic: TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAGgtaggttttt ... catgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
EST: gi|71862348|gb|DT011403.1|DT011403
EST:     TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG                         GCTAGGGTCCCTGTTGGGAAGCGTATCTT
genomic: TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAGgtaggttttt ... catgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTT
EST: gi|110391337|gb|EC956303.1|EC956303
EST:     TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG                         GTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
genomic: TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAGgtaggttttt ... catgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
EST: gi|34546915|gb|CF515147.1|CF515147
EST:     TGACCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG                         GCTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
genomic: TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAGgtaggttttt ... catgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
EST: gi|110422883|gb|EC989216.1|EC989216
EST:     TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG                         GCTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG
genomic: TGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAGgtaggttttt ... catgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAG
                           ctctgac  putative branch site (score: 3)
     aatgcttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttttcatgttcatcagtgttctttatgatgcactacttcaatttcctgaacaattaatcaattgttatcttagaaattaaaaaaaaaaaggagagagaaataactatttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC