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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATAATGGCTGAAGGAAAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaactacattatcatgctttcttgtacagaagtcaggcatttgtatttgtatgtttttgttaatatttacaaagagggaaagcataatacaac...

Basic information

species Vitis vinifera
transcript Vv14s0060g01920.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G180990_T02 (Zea mays), 5'ss of exon 6
GCCATAATGGCTGAAGGAAAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaactacattatcatgctttcttgtacagaagtcaggcatttgtatttgtatgtttttgttaatatttacaaagagggaaagcataatacaac---
|| ||||||||||||||||| ||||| || || || ||||| |  ||||| ||||||||||||||||||||||||  |||      |  || ||  |  |   | | ||| |   | | | |  ||          ||    | ||   | |     |     ||      
GCTATAATGGCTGAAGGAAAACAACACGCCCTGGCAATTGGATATACAAAGATGTCAGCAAAAGACATgtaagtttcactctgaagtattgattaatattg--gcactcaagt-ctcgaagtaatactccaagcacaaagcctgcactcatgctcgtctccgcactctttt

upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G41130.1 (Glycine max), 5'ss of exon 5
GCCATAATGGCTGAAGGAAAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaactacattatcatgctttct---tgtacagaagtcaggcatttgtatttgtatgtttttgttaatatttacaaagagggaaagcataatacaac-
||||| |||||||||||||| || ||||||||||||||||| || ||||||||||||||||||||||||||||  ||  | |||||||     || |   || |||| | |   | ||    ||   ||||  ||| ||   | | | ||  || ||     | | | |   
GCCATCATGGCTGAAGGAAAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaaga-aacttgcattatctcatcttttgactggacaggaatgttgaatgaa-ataaatatgaatttttt--cactaataagcagagactctgtcagatattc

upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G13720.1 (Glycine max), 5'ss of exon 6
GCCATAATGGCTGAAGGAAAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaactacattatcatgctttcttgtacagaagtcaggcatttgtatttgtatgtttttg--ttaatatttacaaagagggaaagcataatacaac--
||||| ||||||||||| || || ||||||||||||||||| || ||||||||||| ||||||||||||||||  ||  |  ||||||     || ||    |   | |||| || |  | |   ||   | ||  ||   | | | ||| || ||     | | | |    
GCCATCATGGCTGAAGGTAAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCTGCAAAAGACATgtaaga-aacttgtattatctcatcttttt---tattgggcaggaatgttgaatgaaataaatatgaattgtcactaataaacagagactctgtcagatactcc

upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G09150.1 (Arabidopsis thaliana), 5'ss of exon 7
GCCATAATGGCTGAAGGAAAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaactacattatcatgctttcttgtacagaagtcaggcatttgtatttgtatgtttttgttaatatttacaaagagggaaag-cataatacaac-----
||||||   || |||||||||||||||||  | || || || ||||| |||||||||||||| ||||||||||| ||  |      |     ||  |||   | ||  ||  ||| ||  ||  |||  ||| ||  || ||  | || |   |    | |    | |      
GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAAATGTCAGCAAAGGACATgtaagtcaatttttcgc-tggaatttatttg---aaaatacaaacatgtgctttgatatactttcgt--atcttagccaaaatacagtctcttggctccaggcctc

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|30132447|gb|CB917786.1|CB917786
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAGCAATCAACAAAGG
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGG
EST: gi|110697600|gb|EE074740.1|EE074740
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|110722653|gb|EE099067.1|EE099067
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAACAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|87584110|gb|DY473391.1|DY473391
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         AAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|45368131|gb|CK906490.1|CK906490
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         AAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|110690622|gb|EE067882.1|EE067882
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|32458352|gb|CD799526.1|CD799526
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         AAGAGCAATCAACAAGGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|83276359|gb|DV940367.1|DV940367
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         AAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|30297956|gb|CB974750.1|CB974750
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|110387074|gb|EC951714.1|EC951714
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
EST: gi|51050864|gb|CO818767.1|CO818767
EST:     AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACAT                         TAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA
genomic: AAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaa ... gcgactgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATAATGGCTGAAGGAAAGCAACATGCTCTTGCTATTGGGTTCACAAAAATGTCAGCAAAAGACATgtaagttaaactacattatcatgctttcttgtacagaagtcaggcatttgtatttgtatgtttttgttaatatttacaaagagggaaagcataatacaac

- - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agggaaa