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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctccttttctccctttctctctttctctctttctaatgtgttatatgttcatctgcttcttgattaatgtttaatacttttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT

Basic information

species Vitis vinifera
transcript Vv00s0187g00340.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G01270.2 (Glycine max), 3'ss of exon 11
tctctccttttctccctttctctctttctctctttctaatgtgttatatgttcatctgcttcttgat----taatgtttaatactt-ttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT---
    ||  | |     || ||  |  |  |   |   ||   ||||||  || |     || |  ||     ||    |   |||| ||||| |||   |  ||||||||||||| |||| ||||||||||| |||||||||||||| ||||||||| | |||||||||||||||||||||||||| ||  | ||||| |||   
---ttctatctgataattgcttgcccttgcctatgagaaaaagttatactttgaaacagttatacataatacaaaaaatcccacttattctacctctctg--tagATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTGTA

upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 11
tctctccttttctccctttctctctttctctctttctaatgtgttatatgttcatctgcttcttgat----taatgtttaatactt-ttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT
    ||  | |     || ||  |  |  |   |   ||   ||||||  || |     || |  ||     ||    |   |||| ||||| |||   |  ||||||||||||| |||| ||||||||||| |||||||||||||| ||||||||| | |||||||||||||||||||||||||| ||  | ||||| |||
---ttctatctgataattgcttgcccttgcctatgagaaaaagttatactttgaaacagttatacataatacaaaaaatcccacttattctacctctctg--tagATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT

upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G12100.1 (Glycine max), 3'ss of exon 11
tctctccttttctccctttctctctttctctctttctaatgtgttatatgttcatctgcttcttgatta-----atgtttaatactt-ttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT
    ||| |       || ||  |  |  |   ||  |    ||||||  || |     || |  || |     |    | | |||| ||||  ||| | |  ||||||||||||| |||| ||||||||||| |||||||||||||| ||||||||| | ||||||||||||||||| |||||||| ||  | ||||| |||
----tccatcgtataattgcttgcccttgcctattagagaaagttatactttgaaacagttatacataatacaaaaaaatcacacttgttctgcctctttg--tagATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT

upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G12050.1 (Arabidopsis thaliana), 3'ss of exon 11
tctctccttttctccctttctctctttctctctttctaatgtgttatatgttcatctgcttcttgattaatgtttaatacttttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT
            |   || |||| |      ||  | ||| |  |  || |   |   |   ||| || |     ||  |||||  |  |  ||  | |||||||||||  | || || || || |||||||||||  | || |||||||| || ||||| || ||||||||||| || ||||||||||| ||||| 
-----------gtgagttcctctataatctcctacccaat-tcctccatataattaaacagtttggttca-----aactcttttaaacttattgtgacagATATTGGACCATAACGCAGCAGCTAGCACACCATACCGTTAACGGTTGCAATTTGAGGCCTGGTGATCTCCTTGGCACAGGAACCATAAGCGGACCG

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|110690312|gb|EE067299.1|EE067299
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|161719983|gb|FC067725.1|FC067725
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGT
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGT
EST: gi|37187151|gb|CF606504.1|CF606504
EST:     TGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: TGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110363209|gb|EC926783.1|EC926783
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110402111|gb|EC968746.1|EC968746
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110361741|gb|EC925237.1|EC925237
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|161721615|gb|FC070825.1|FC070825
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTT
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTT
EST: gi|110364853|gb|EC928407.1|EC928407
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110372453|gb|EC936619.1|EC936619
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110392090|gb|EC957263.1|EC957263
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTG
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTG
EST: gi|45771743|gb|CN007595.1|CN007595
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110702040|gb|EE080300.1|EE080300
EST:     GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GCTGGACATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|37187213|gb|CF606566.1|CF606566
EST:     TGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: TGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|110361518|gb|EC924998.1|EC924998
EST:     GTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: GTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
EST: gi|37189933|gb|CF609282.1|CF609282
EST:     ATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTT                         ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA
genomic: ATAAAAATTCGTGCATTGTCACAAGGAGTAACTTAAAGCACTTgtaaggattt ... catggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgttcatctgcttcttgattaatgtttaatacttttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT
                                tacttttctatctc  CT-rich tract
                    attaatgtttaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctccttttctccctttctctctttctctctttctaatgtgttatatgttcatctgcttcttgattaatgtttaatacttttctatctcatggaatagATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA