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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaatttcattctgtcctaaaagttataatgcttctcataagaaaaaaaggtcattgtgaggactctttattttttacat...

Basic information

species Vitis vinifera
transcript Vv13s0147g00220.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 3
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaatttcattctgtcctaaa---agttataatgcttctcataagaaaaaaaggtcattgtgaggactctttattttttacat-----------------
  |||||   ||  | ||||||||||||||||| |||||   || |||||| || || ||||| ||||||||||| || || ||||| ||  ||||||||||| | |        || |       ||  | ||  || |      |||  ||   | || |||  |  ||   |  ||||         ||||||| | |                   
AATTCCACAGCCAGTTGTTCTGATAGATCAAGACTCAGACCGTGATGCAACCATAGTGCAGCTGAGTTTTGGAGACCGTCTGGGGGCACTACTTGACACGgtataattttcctatgctatgggtgctctatttgatctgatcttgtttaagatatatttcgtaattagtaatttttgttgtatcagtaaattattttgtcctggtattcactgtttgcag

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G066496_T01 (Zea mays), 5'ss of exon 3
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagag---------taactactagcaagtcaatttcattctgtc----ctaaaagttataatgcttc------tcataagaaaaaaaggtcattgtgaggactctttattttttacat
  | |||   ||  | || | |||||||||||| |||||   || |||||| ||||| ||||| ||||||||||||||  | |||||  |  ||||||||||| |          | || |||      |    || |   |||     || |||  | |  || ||       || | | |        | ||| ||     | || | | ||| || 
AATCCCAGTCCCAGTTGTCCAGATAGATCAAGACTCAGACCGTGATGCAACCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCATTACTTGACACGgtatatattttacattcaccactgatgctttgtctttacattgtggctgctcaaaactgtgttgttttacattttcgtcatatctgccaattattttgcctggtattcactgtttgcag

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G066496_T02 (Zea mays), 5'ss of exon 3
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaatttcattctgtcctaaaagttataatgcttctcataagaaaaaaaggtcattgtgaggactctttattttttacat----------
  | |||   ||  | || | |||||||||||| |||||   || |||||| ||||| ||||| ||||||||||||||  | |||||  |  ||||||||||| |     |||   ||   || |     | |||| | | | || |   ||| ||||     |||    ||  || |      || | || | |  ||           
AATCCCAGTCCCAGTTGTCCAGATAGATCAAGACTCAGACCGTGATGCAACCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCATTACTTGACACGgtatatattttacattca--ccactgatgctttgtctttaca-ttgtg--gctgctca-----aaactgtgttgttttacattttcgtcatatctgccaattattttgcc

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G42580.4 (Glycine max), 5'ss of exon 3
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaatttcattctgtcctaaaagttataatgcttctcataag---aaaaaaaggtcattgtgaggactctttattttttacat
|||||| |  || || ||||| ||||||||||| ||||||||||  ||||||||||| |||||||| ||||| ||||| ||||| |||||| ||||||||||    |  ||||| | || | ||||      | ||| |||  |   ||    |   |||      |    | ||| ||     |    ||| || ||||   
TGTTCCTATGCCAATAGTTCTAATAGATCAAGAATCAGATTCTGAAGCAACAATTGTGCAGCTTAGCTTTGGGGATCGCCTTGGAGCTCTTCTTGACACGgtgatttggctactggaaactaaattatgcaatctccaaaatttccaaaccagttggatatctttgatgggatgtcctttaactgcaattttgttattta---

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G24450.1 (Glycine max), 5'ss of exon 3
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaatttcattctgtcctaaaagttataatgcttctcataagaaaaaaaggtcattgtgaggactctttattttttacat
| |||| |  || || ||||| ||||||||||| ||||||||||  ||||||||||| |||||||| |||||  |||| ||||| |||||| ||||||||||    |  ||||| | || | ||||      | ||  | |  ||  ||    | | |||   |  ||  |  ||| ||     |   |  |  |  || 
TCTTCCTATGCCAATAGTTCTAATAGATCAAGAATCAGATTCTGAAGCAACAATTGTGCAGCTTAGCTTTGGGAATCGCCTTGGAGCTCTTCTTGACACGgtgatttggctactggaaactaaattatgcaatctctaagattttcaaaccagtttgatatccattaactgcaattttgttatttaagtgatgctctcac

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G04740.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaa----tttcattctgtccta----------aaagttataatgcttctcataagaaaaaaaggtcattgtgaggactctttattt-tttacat----------------------------------
||||||||  || |||||| ||||||| || ||| | ||  |||  || || |||||||| || ||||||||| |||| |||||||||||| ||||||| ||   | |     || |  ||       |||  |||| || ||          |||  | ||    ||||        |      | | | | || |     | |    || | |                                  
TGTTCCAATGCCAATGGTTATGATAGACCAGGATGCTGACCCTGAAGCTACTATTGTACAACTCAGTTTTGGAAATCGTCTTGGGGCTCTTATTGACACAgtgagggattctatatcctgttttggttttttgttctatcttatcgatgtgaaaaaactttagcttttcttgatttgtagcgtttttactatcagaatcagatgtaaacttgccttgttttcggcttatgaatcatatgtgtgtggcag

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|22014312|gb|BQ799346.1|BQ799346
EST:     CAATTGTACAGCTTAGTTTCGGAGATCGACTTGGGGCTCTGGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|110392201|gb|EC957452.1|EC957452
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|110359925|gb|EC922269.1|EC922269
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|22014843|gb|BQ799877.1|BQ799877
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|22014313|gb|BQ799347.1|BQ799347
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|22014315|gb|BQ799349.1|BQ799349
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|110430431|gb|EC996990.1|EC996990
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|110394001|gb|EC958326.1|EC958326
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
EST: gi|110358677|gb|EC923071.1|EC923071
EST:     CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACG                         ATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG
genomic: CAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaac ... gtcatggcagATGAAGGCTTTGAAAGGTTTAGATCTAGATGTGCAAAAGGGAACTGTTACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGACTTGGGGCTCTTGTTGACACGgtagagtaactactagcaagtcaatttcattctgtcctaaaagttataatgcttctcataagaaaaaaaggtcattgtgaggactctttattttttacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa