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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA

Basic information

species Vitis vinifera
transcript Vv13s0074g00140.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgt-tagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
                                                                               |||    |||  |  ||| |      |  ||      | | |||  | |           |   |||  ||       ||| ||| ||  || || ||  || |  |||| ||||| |||||||| || ||||||||| | ||||| |||||||| || |||||| | |||||||||||||| |||||||| || ||||| || ||||
------------------------------------------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagtta----------gggggtcttttg-----catacaatttc--aagtgttctcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgt-tagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
                                                                                       |     | || |  ||    || | |  ||  | |   | | ||| | | || |         ||  ||  | ||| |     |||| |  |||||  |||| || || ||||| || |||||||||||| | ||||| |||||||| || |||||| |||||||||||||||| || ||||| || ||||| || ||||
--------------------------------------------------------------------------------------gtcaggctgttcatcgaa---tgattgctttaatgtcaggatatttctctgcttag--------aaggttgttgtaaacgt---attggtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 3
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgcttttt----atattctgaatgtccattaatatttatataatctcgtaattgatcaattgt-tagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
                                                                                                            |||    | | |||  |  ||||     | ||    ||  |     ||| ||  |||        | |  ||   || | ||||| || || |||||||| |||||||||||| | ||||| |||||||| || |||||| |||||||||||||||| || ||||| || ||||| || ||||
------------------------------------------------------------------------------------------------------------gttac--tagctatcatatttttgtaagagatgtctaagattataaaatcttcttatggaaagaaactacatatgttttatagGTTTTCCTTTTTGCCAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 2
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
                                                                                                        |  ||||    || |    | | ||| ||   |   |       ||  |  |   |  | ||   | ||| || ||    |||| || || |||||||| || ||||||||| | ||||| |||||||| || |||||| |||||||||||||||| || ||||| || ||||| || ||||
--------------------------------------------------------------------------------------------------gttactcgctgttacatttttataagagatttataagcttatagaaaatgtttgttatggaaagaacttacatttgttctat----agGTCTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G074898_T01 (Zea mays), 3'ss of exon 3
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgt-gctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgtt--agGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
                                                                                                           ||||    || || |  | | ||| ||   | |  ||  |     ||  |  |||      | |||  |||  || ||  |||| || || |||||||| || ||||||||| | ||||| |||||||| || |||||| |||||||||||||||| || ||||| || ||||| || ||||
--------------------------------------------------------------------------------------------------gttacttgctgttacattttttgtaataggtttgtaagctttatatagc-----atgatcttatggcaaggaaatacatctgtttttgtagGTTTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 2
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttcct-tgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataat--ctcgtaattgatcaattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
        |||   | || ||  | |  |  | | |    || || |   || |  |   ||   | |      || || ||||| || ||||||       || || | ||       |||| | | ||||| | || | | |    ||  ||| | |||| |    |  |  ||| | |||   ||||| || || |||||||| |||||||| ||| | || || |||||||| || ||||| |||||||| |||||||| |||||||| ||||||||||| || |
--------gtgacataaaatatgtctcattgaattttgggtggatgt---atctcatcatttcagtct----ggatgttcaatttgctatgattt-------gatcatttttaa-----ttatggggttttttct-ttgttactagttat-gatactgatatgagggtttttgtttgttgaatctatagGTTTTCCTGTTTGCCAACTCAAAATGTAAGCGGTATTTCCACAACCGCCTGAAGCCCTCAAAGCTCACCTGGACTGCTATGTACAGAAAGCAACACAAAA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G37370.2 (Glycine max), 3'ss of exon 2
gtaaaaatgtggatttaattacatattttcaagtctcatatga-atatttaatttgcttgattgc-ctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
             |   || | |||| ||   |  | || ||    |||   |  |  || |||  || |    ||  || | ||    ||   ||| |||    |  || ||  | |||||     |||  ||||  | |  ||    | | ||||    ||  | | ||  ||| | |||    |||| || || ||||| || |||||||| ||||| || || ||||| || || |||||||||||||| |||||||| || ||||| ||||||||||| || |
------------gtaacataaaatatgttttgggttgatgtgtcgcattatttcagtctggttgttctgtttgcaatgatgtgatcatttt---ttagttatgagg--gttttttgtttgtt-----gctagttatgatattgat----actgatatgaggat--ttttgt--ttgttgaatctacagGTTTTCCTGTTTGCAAACTCAAAATGTAAGAGGTATTTCCACAATCGCCTGAAGCCTTCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAAA

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|37188150|gb|CF607501.1|CF607501
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|22011818|gb|BQ796852.1|BQ796852
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|71868597|gb|DT017652.1|DT017652
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|77581842|gb|DV219879.1|DV219879
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|71873024|gb|DT022079.1|DT022079
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|110384865|gb|EC949331.1|EC949331
EST:     CTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|71866495|gb|DT015550.1|DT015550
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|30136747|gb|CB922085.1|CB922085
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|110359284|gb|EC920528.1|EC920528
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
EST: gi|110363994|gb|EC927631.1|EC927631
EST:     CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAG                         GTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT
genomic: CAAAGATATACCCTGGTAAAGGTATCAGATTTGTTAGATCTGATTCACAGgtaaaaatgt ... caattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattctgaatgtccattaatatttatataatctcgtaattgatcaattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA
                attaatatttatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgttagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA