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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC

Basic information

species Vitis vinifera
transcript Vv12s0057g01480.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcatta--ccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
                       |||   | |  ||||||     ||   |  |||| |||| |  |     |||||||| || | ||| |     |  |   |     |   |    ||||||||||| ||||||||  |  |||| || || ||||||||||| ||||| ||||| ||  | |||||||||||||| || || |||||||||||||| || 
-----------------------gtaaggtttacattttgcatggtgaaaacaagttacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgat--gcagtttatgatattaa-tatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
          |  |  |||   | || ||  ||  | | | |     ||    | |||    |||      |||| | ||   |   ||||||||| || |||    |  || |  |  ||||| ||||| ||||| ||  ||||||| || || ||||||||| | ||||| || || ||| | |||||||||||||| || || ||||| |||||||| || 
--------gtatgctttcaatttttacaccttgc-tgtggctgaagattatggaatttgaagcatg--tgaatttataattgtctccttatgatataaaatataccatcaaaat--atctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
------gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgata--ttaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
        | ||| ||  | ||     ||| |    |  | ||   |   |       ||      |  | |   | | ||   ||  |||   || |   |||   |     |  | |   | | ||||||||| ||||||||  |||||||||| || ||||||||| || |||| || || ||| | |||||||||||||| || || ||||||||||||||||| 
gtatgcacattttcacttctcactgtgctgca-gtagaaagttacaacgcc------gcatgcgtgtcaaatcttataatttcaat-tagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 5
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
                       ||||  | || |     || |||    || ||||    |  || | |  ||   |||      ||  |  |   | || |     | |     | ||||||||| || |||||  ||||||| || || |||||| |||||||||| || || ||| | |||||||||||||| || || ||||||||||| || || 
-----------------------gtatggtttgtac----atgtctacataa-agttaagat-gttgcaattttctagat-----ctaccacttacctttgatcaaacattctgtatacagCTTCTATGATCGTTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGG

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
--gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgata--ttaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
   |  ||| ||  | ||     ||| |   ||  | ||   | | |||     ||      |  | |   ||| ||   ||  ||||  |  |   ||| | |     | || |   | | ||||||||| |||||||   ||||||| || || ||||||||| |  |||| || || ||| | |||||||||||||| || || |||||||||||||| || 
gtatgctttcacttctcactgtgctgca-gttggaagttgcaa-cgctg-----catgcatatcaagtcttacaatttcaat-tagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
|||  ||    ||| ||  ||   ||||      || ||||    |||    || |     |  ||       ||||||||   |||||| | || ||  | ||| | |  |  ||||||| ||||| || ||||| |||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||||||||||| || 
gtaaatt----gcctatttga---tatatccatcatattgacaaatgtatttcaatgatagtgttt--tgtggttctgatg---tttatg-tgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
gtag-ttttacagcccatcagactgtatactgtgaattttgatctctgtt-caacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
|||  || || || | ||   | | ||| |     |||   |  | | || |||| ||    |     |      ||||||||   |||||| | || ||    ||| | |  |  ||||||| ||||| || ||||| |||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||||||||||| || 
gtaaattatataggctatttaa-tatatccatcatattgacaaatgtatttcaacggtagtat-----attgtggttctgatg---tttatg-tgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgatattaatatggt--tttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
                                                   |||||  |   |||||| ||| |    ||    | |     |||| |    |  | |||| |     ||||| ||||| ||||||||  |||| |||||||| || || || ||||| || || ||||||||||||||||||||||| || || ||||| || || ||||||
-------------------------------------------------gtacagtaaccg-cattactacactctctattgtatctgaatgattacttaacttatctgaattcttgatgcagTTTCTATGACCGTTCTGCTCCGATCTACACACAGCCGCGTTATTTACCACCGTCTAAGATGCTTGATGCTGATGTTACTGACAGTGTCATCGGAGAGGGC

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|33409675|gb|CF215302.1|CF215302
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|110688952|gb|EE068088.1|EE068088
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|161718175|gb|FC065663.1|FC065663
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|110689182|gb|EE065182.1|EE065182
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAAAATTCAA                         CTT-TCATGACCGTTCCTCTCCAATCTAAACCCAAC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCT-ACGACCGTTCCTCTCCAATCTACACCCAAC
EST: gi|110378789|gb|EC943937.1|EC943937
EST:     AAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: AAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|352777901|gb|FQ466954.1|FQ466954
EST:     AATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTTTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: AATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|71889085|gb|DT038140.1|DT038140
EST:     GCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: GCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|352776770|gb|FQ472657.1|FQ472657
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|30324817|gb|CD008079.1|CD008079
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTC
EST: gi|32245488|gb|CD711307.1|CD711307
EST:     GTGCCAGATTTCAG                         CTTTTATGACCGTTCCTCTCCAATNTACACCCAACCTCGATATTTGCCCCC
genomic: GTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|71863688|gb|DT012743.1|DT012743
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTG
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTG
EST: gi|30324290|gb|CD007552.1|CD007552
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTAC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTAC
EST: gi|32245967|gb|CD711786.1|CD711786
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|33403137|gb|CF208764.1|CF208764
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
EST: gi|30253354|gb|CB970905.1|CB970905
EST:     TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAG                         CTTCTATGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC
genomic: TTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttac ... taaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC
                         tattaat  putative branch site (score: 2)
                        atattaatatggtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT