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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattccctattggcatcttttcttgatgattacaaatccgtgcatgtttcttacaagtaaaacatcgagattctacaggatatagatgga...

Basic information

species Vitis vinifera
transcript Vv17s0000g05880.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g16550.1 (Oryza sativa), 5'ss of exon 2
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattccctattggcatcttttcttgatgattacaaatccgtg--catgtttcttaca-agtaaaacatcgagattctacaggatatagatgga
 ||||| ||| |||||||||||||||||||  | |||||||||||||| || |||||||| |||||||| |||||||| || || ||||||||||||||||||   |||| | ||   |       |||  |||| |  |   |  | | ||  ||||  ||    | | || |   |  | || ||||    |    |    
CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttttgactctagaactattacttgccttgttagtatgagcttcatgaccatgaatcagggatactagacttttaatatgctacttttttagaac---

upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G068489_T02 (Zea mays), 5'ss of exon 1
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattccctattggcatcttttcttgatgattacaaatccgtgcatgtttcttacaagtaaaacatcg----agattctacaggatatagatgga
 ||||||||| |||||||| ||||||||||  | || ||||||||||| || |||||||| |||||||| || |||||||| || |||||||| |||||||||   |||| | ||   |   | ||       |      ||  | |     ||||    |   ||  | || ||      || | || |  |  | | |    
CCATATTACCAGAGGTGAACATGATGAGGATGCTCGATACCCAGAGACTAAGACACTTACAATTGGTCAGTTTAAGCTTGGGCTGTGCCATGGCCATCAGgtttgtttttgactcagaaaatgtataggaggctaggagctattagttt---catgcccatggtaataataatatttttacaggtgctccttgtcacacaaaa-

upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G109315_T02 (Zea mays), 5'ss of exon 2
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattccctattggcatcttttcttgatgattacaa----atccgtgcatgtttcttacaagtaaaacatcgagattctacaggatatagatgga
 || |||||  ||||||||||||||||| |  | || ||||||||||| || |||||||| |||||||| || |||||||| || ||||||||||||||||||   |||| | ||   |   |  | |  |    ||| | | ||    || | | || ||            | | |  ||   | | |  | | ||      
CCACATTACTGGAGGTGAATATGATGAGTATGCTCGATACCCAGAGACTAAGACACTTACAATTGGTCAGTTTAAGCTTGGGCTGTGCCATGGTCATCAGgtttgtttttgactcagcaaatgtctttcatgcccatggtaataatagtattcttacaggtgctccttggcgcacaaaaggaacctatgcttgttttatg----

upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G43610.2 (Glycine max), 5'ss of exon 4
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattcc----ctattggcatcttttcttgatgattacaaatccgtgcatgtttcttacaagtaaaacatcgagattctacaggatatagatgga
|||||| || || ||||| ||||| || ||||||   || || |||||||||||||| |||||||| ||||| ||||| |||||||||||||||||||||||   ||||| |  |      |||| ||    ||| ||  | | |  |  |  |   ||       |   || || |||   ||   |||    | |       
GCATATAACTCGTGGTGAGTATGACGAAGAGACAAAATATCCGGAGACCAAAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAGgtctgattttgagactgatattatttgccctgttttttcttaaatggacctaagaaaattgggagcatgggtgaatcataaggaaattaccttttttctt----

upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA14G05340.2 (Glycine max), 5'ss of exon 3
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattcc----ctattggc---atcttttcttgatgattacaaatccgtgcatgtttcttacaagtaaaacat--cgagattctacaggatatagatgga
|||||| || || ||||| |||||||| |||||    || || |||||||||||||| |||||||| ||||| ||||| |||||||||||||| ||||||||   ||||| | ||      |||| ||    | |||| ||  | | |  |  |  |   ||            | || |||  ||| |||      |||         
GCATATAACTCGTGGTGAGTATGATGAAGAGACGAAATATCCGGAGACCAAAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgattttgactctgatattatttgccctgtttttttttcttaaatggacctaagaaaattgggagcgtggatgaatcataacgaaattacctttgat---------

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|32267465|gb|CD716428.1|CD716428
EST:     AAACACTGACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTGGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|71890537|gb|DT039592.1|DT039592
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|32272444|gb|CD721603.1|CD721603
EST:     AAACACTGACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTGGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|32247405|gb|CD713224.1|CD713224
EST:     AAACACTGACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTGGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|110732723|gb|EE108257.1|EE108257
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|32265181|gb|CD716770.1|CD716770
EST:     AAACACTGACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTGGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|110732750|gb|EE108311.1|EE108311
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|34320397|gb|CF373151.1|CF373151
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|110383433|gb|EC947806.1|EC947806
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|33401447|gb|CF207074.1|CF207074
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
EST: gi|71890549|gb|DT039604.1|DT039604
EST:     AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG
genomic: AAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaatttt ... tgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattccctattggcatcttttcttgatgattacaaatccgtgcatgtttcttacaagtaaaacatcgagattctacaggatatagatgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggata