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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcattttgtggggggaattagtttgcaaaatctgcaactgctcttcaagtgcagtttgggttacatgtaagcattgagttccttgacataagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCAACGAGTTTTGGTTACTTAGAGATAAGTTGATACCAATCAATGATACAGT

Basic information

species Vitis vinifera
transcript Vv07s0130g00170.t01
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ13811 (Selaginella moellendorffii), 3'ss of exon 6
tgcattttgtggggggaattagtttgcaaaatctgcaactgctcttcaagtgcagtttgggttacatgtaagcattgagt-tccttgacataagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCAACGAGTTTTGGTTACTTAGAGATAAGTTGATACCAATCAATGATACAGT
                                       |   ||||    ||   ||   || |   |   | |||  | ||||||||||    |  ||||||| ||  | ||    |   || | || || |||||||||||||||||||||||||||||| ||||  | || ||| ||||||  |||||||| || | 
--------------------------------------gtatccttccttggcctgtta--ttgcgcat---ccttggttatccttgacatt--tttgcagACTTAAACTTTGAAGAGACATCAGGAAACTATTATCCTACCGTTTTCTTCAACGAGTTTTGGCTACTGCGCGACAAGCTGATACGCATCAATGAGACGGC

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 6
tgcattttgtggggggaattagtttgcaaaatctgcaactgctcttcaagtgcagtttgggttacatgtaagcattgagt-tccttgacataagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCAACGAGTTTTGGTTACTTAGAGATAAGTTGATACCAATCAATGATACAGT
                                       |   ||||    ||   ||   || |   |   | |||  | ||||||||||    |  ||||||| ||  | ||    |   || | || || |||||||||||||||||||||||||||||| ||||  | || ||| ||||||  |||||||| ||   
--------------------------------------gtatccttccttggcctgtta--ttgcgcat---ccttggttatccttgacatt--tttgcagACTTAAACTTTGAAGAGACATCAGGAAACTATTATCCTACCGTTTTCTTCAACGAGTTTTGGCTACTGCGCGACAAGCTGATACGCATCAATGAGACGAC
















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|110701765|gb|EE079713.1|EE079713
EST:     ATATTCACAAAATGGCGTTCCANCAAATATTGCTCCTT                         ACTTGAATGTGGAGCCTAGTACAAGGA
genomic: ATATTCACAAAATGGCGTTCCACCAAATATTGCTCCTTgtatccttga ... aagatcacagACTTGAATGTGGAGCCTAGTACAAGGA
EST: gi|110712610|gb|EE087807.1|EE087807
EST:     ATATTCACAAAATGGCGTTCCACCAAATATTGCTCCTT                         ACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCA
genomic: ATATTCACAAAATGGCGTTCCACCAAATATTGCTCCTTgtatccttga ... aagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCA
EST: gi|110701816|gb|EE079820.1|EE079820
EST:     AAATGGCGTTCCACCAAATATTGCTCCTT                         ACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCA
genomic: AAATGGCGTTCCACCAAATATTGCTCCTTgtatccttga ... aagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagtgcagtttgggttacatgtaagcattgagttccttgacataagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCAACGAGTTTTGGTTACTTAGAGATAAGTTGATACCAATCAATGATACAGT
                                  ttccttgac  putative branch site 
                                           ataagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcattttgtggggggaattagtttgcaaaatctgcaactgctcttcaagtgcagtttgggttacatgtaagcattgagttccttgacataagatcacagACTTGAATGTGGAGCCTAGTACAAGGAATTACTATCCTACCGTTTTCTTCAACGAGTTTTGGTTACTTAGAGATAAGTTGATACCAATCAATGATACAGT

- - - - gtggggg
- - - - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - -tgcaact
- - - - - - - - - - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccttg