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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC

Basic information

species Vitis vinifera
transcript Vv06s0004g04430.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
   |   | ||  |  | || |  |   || || |  |     |  ||     |||   || ||  || | |  |  | |    | |  |||||||||| |||||||| |||||||| || ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||| ||||  ||| | |||||
---gtcagctttcctcattgtaacttcatgtttctgtaactccatgatc----cataattttaacacagcataatattggt-caattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactc--ttaccattggagcatggcttgaaatcaac--ttggttcttgcatgaatta-cagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
                   | | |  |     |  || ||    ||| ||| || |||| |         ||  ||  || |    ||||||  |||||||||| |||||||| || ||||| || ||||| ||||| |||||||| || || ||||| |||||||||||||| || || ||||  ||| | || ||
-------------------gtaagcatcgctatcatgtcttgtctactatttgatcatgccaaagttctgacaattctttttgttttgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
   |   | ||  | | | |  |||  |    | |    ||| | |||     ||  | |   |  ||| |    |  |     | |  |||||||||| ||||| || || ||||| || ||||| ||||| |||||||| || || | ||| |||||||||||||| || || ||||  ||| | || ||
---gtaagcttcactatcggactgtactcatgtctactatctgatcat---gtcaaagttctga--caattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatca-acttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
||  | | ||| |   | || |  | | |  || || |||    |    |     |    ||| ||||  | |  |  |||    ||   |||| ||||| ||||| || || || || || ||||| ||||| |||||||| || ||||| || |||||||| ||||||||||| ||||  ||  | || ||
gtcagctttttatt--agtgaaaat-tgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatca-acttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
||  | | ||| |   | || | || | |  || || | | |  ||  ||     |    ||| ||||  | |  |  |||    |||  |||||||| ||||||| |  || || || || ||||| ||||| |||||||| || |||| ||| |||||||| ||||||||||| ||||  ||  | |||||
gtaagatttttatt--agtgaaagt-tgtatttatttagtttatccgctgttatgttttctgacatcatgcatattatttggggaaatgccagTTTATTCAGATGGGCTGGTGTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAGTGGTTATGAGCTCGCAAGTGAGCGTTGGACACCTGTGCATAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
       ||| |||  ||  ||| | ||| ||      ||  | | |||    ||||     || ||||    | | |||    | || |||| ||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||||| |||  | |||||
-------gttggtctgac-acattttttttatc-----ctgcttcgattaatacatga----aattcaat---gatgttgttcaatttgcagTGTATCCTGATGGGCGAGTTTGCATATCAATTCTTCATCCTCCTGGTGACGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
||| ||| ||| |         |||| ||    |||||     || |   ||   ||    |  ||       ||||    |    || |||| ||||| ||||| || || |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||||||||||||  ||  | |||||
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttc----aatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactc-ttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
       ||| ||    || |||   ||| ||||||  ||   |   ||||   ||||      ||| ||    | | || |||   || |||| || || ||||| ||||| |||||||||||||| ||||| || ||||| ||||||||||| ||||||||||||||||||||||||| |||  | |||||
-------gttggtttggct-cat---ttttatttttatcttgctttgattgatacatgat----aatgaatgatgctgttccat---ttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 3
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
||| ||  ||| |   | |   ||  ||||   ||||| |   || |   ||   ||   ||   ||   |   || |||||         || ||||| ||||| || || |||||||||||||| ||||||||||||||||| |||||||| || |||||||| |||||||||||||  ||  | |||||
gttagtgttttttttgaatttgtgattttg--ctttgatttgaactacatgaaagtga--tgttttctgttcaatttttgca---------gTATATCCCGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTACGAGCTTGCGAGTGAGCGCTGGACACCTGTTCATAC

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|110710545|gb|EE086990.1|EE086990
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110364996|gb|EC928664.1|EC928664
EST:     GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110427457|gb|EC993894.1|EC993894
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110407296|gb|EC972893.1|EC972893
EST:     GTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110696034|gb|EE074731.1|EE074731
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110695874|gb|EE074387.1|EE074387
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110706251|gb|EE081613.1|EE081613
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110693589|gb|EE069952.1|EE069952
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110376683|gb|EC941750.1|EC941750
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|110696006|gb|EE074671.1|EE074671
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
EST: gi|30124774|gb|CB910113.1|CB910113
EST:     AAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG                         TTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG
genomic: GAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATGgttggttgtt ... tgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
 ctcttac  putative branch site (score: 3)
                                            atgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA