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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttctccaattgaactccaaatttcatatttctatcttttttattgaattgaaactttagagattttgattggtgaaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG

Basic information

species Vitis vinifera
transcript Vv14s0068g01280.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 2
gtaaaatttc-tccaattgaactccaaatttcatatttctatcttttttattgaattgaaactttagagattttgattggtgaaatttac-agTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG
|| ||   || | |     || | ||  ||||     |||  | | | |||  | ||     || |     ||    ||       |||  |||| ||||  |||||||||||||| ||||||||||||||||||||||| |||||  | ||||  |  || ||| | || |   | || || || || ||||
gtgaatcctcattccgccaaattacacttttctctgatcttgcgtctctatccatttatttattcacctgcttcctctgtaatgcattattagTCCAACAATTTCGTCGAAGGAGTCACGCACAAGATCAGGCGCCAGATTGAGGAGCTCGAGAGAGTTTCCGGCATCGACAGCGGCGCCCTCACCGTCGATG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 2
gtaaaatttc--tccaattgaactccaaatttcatatttctatcttttttattgaattgaaactttagagattttgattggtgaaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG
|| ||   ||  |||| ||    |||    | || ||  || | | || | |    ||  | ||  |   ||||       |   |||||  ||| ||||  ||||| |||||||| ||||||||||||||||||||||| |||||  | ||||  |  || ||| | || ||  | || || || || || |
gtgaatcctcattccactttttttcctttctccaaatcact-tatcttctctgatctttcatctcca---atttaatgcattattattta--gTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAGGAGCTCGAGAGAGTTTCCGGCATCGACACCGGCGCCCTCACCGTCGACG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------gtaaaatttctccaattgaactccaaatttcatatttctatcttttttattgaattgaaactttagagattttgattg---gtgaaatt-tacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG
                                                           |   ||   |   ||||      ||||| || ||   | |   |   |||  ||| |  ||| |    ||||   ||   |||   |  | ||||| ||||| ||||| || |||||| |||||||||||||||| ||||| |||||  | ||||  |  || ||||||| ||  ||||   | ||||||||||
gtacgtcaaattcccaatcacaccaaaacattcgcgactatttacggttgcggttccgttgcgatccttgatattgtgga--aaattacagataaatgtggctgcaatttcatt-atgcttgatctgttttctgtgtgtgtgtgttcgtgcagTCGAACAGTTTCGTGGAGGGAGTGTCGCACAAGATCAGGCGGCAGATTGAGGAGCTGGAGAGAGTGTCCGGCGTGGTGAGCAGTGGTTTGACGGTGGATG

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|351031454|gb|FQ446657.1|FQ446657
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|349830231|gb|FQ420491.1|FQ420491
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|351024893|gb|FQ433310.1|FQ433310
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|71881861|gb|DT030916.1|DT030916
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|110699022|gb|EE077184.1|EE077184
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|110693329|gb|EE069475.1|EE069475
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|349833078|gb|FQ416456.1|FQ416456
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|71882447|gb|DT031502.1|DT031502
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|27581998|gb|CB004693.1|CB004693
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|161716182|gb|FC069494.1|FC069494
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|352785589|gb|FQ475592.1|FQ475592
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAA                         TCTAACAGCTTCGTCAAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|71883798|gb|DT032853.1|DT032853
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|71858149|gb|DT007204.1|DT007204
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|351020303|gb|FQ445910.1|FQ445910
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|110693330|gb|EE069469.1|EE069469
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|110700866|gb|EE077894.1|EE077894
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|294964114|gb|GW837917.1|GW837917
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
EST: gi|349830278|gb|FQ420538.1|FQ420538
EST:     GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAG                         TCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG
genomic: GTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGgtaaaatttc ... aaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatcttttttattgaattgaaactttagagattttgattggtgaaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG
                                 ttttgat  putative branch site (score: 4)
      ttttttattgaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatttctccaattgaactccaaatttcatatttctatcttttttattgaattgaaactttagagattttgattggtgaaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA