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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG

Basic information

species Vitis vinifera
transcript Vv17s0000g01720.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgct-tctgcctttttgtgtattacaacaattaaagggtaggcg---gtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
                     |    ||| ||  | | ||  |  ||  ||   | | |   |||||   |   |   |||    | ||    ||  |||  |  | | |  ||| | ||  |    |||  | | || ||||| || ||||| ||||| || || |||||||| || ||||||||||||||||||||| | || || || ||||| |||||||
---------------------caaagaaaaatcttgtatgtgtgcttaagttcaaaatctcgtaaagaaaaaatgtatgtacacccgtt-tgcttattctggttttgtgtgatttactttagAAATCGGA--CTTGGAGAAGGCGCAGCTTGGCCTGGGTCATAGCTACAGCAGGGCGAAGGTGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
              | ||   |  |||    |||||      |||  | | || |    || ||| |||        | || ||     |||   |  |    ||| ||||   ||| ||||    ||| | |||||||| || || || ||||| || || || ||||| |||||||| ||||||||||||||| | || ||||| ||||| ||||| |
--------------tgttggactgcaa----tgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgct--cctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttattt---ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
                           |   | |   |  |||||| | |     ||   ||  |  |      |  |  | |    |||||  ||| ||  || | |     ||  ||||||  |   ||| | || |||||||||||||| ||||| || || |||||||| || ||||||||||||||||||||  | || ||||| ||||| || || |
----------------------tgatgagcttacgcattgctttttatatgcctaaattgttgtaaagctaaacgcctgctgtgcttaatttggctt-taccatgtgtccatgttgattgtagGATTCTGACTTGGAGAAGGCCCAACTTGGCCTGGGGCATAGCTACAGCAGGGCTAAGGTGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatat--gcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
                        |||||| |  ||| |||   || ||  || |  | ||| |   |    |  | |   | |||       |   ||    | |    |  |  ||||||  |   ||| | || |||||||| ||||| ||||| || || |||||||| || ||||||||||||||||||||  | || || || ||||| || ||||
----------------------tgcaaaattttggctgctgggcttatgcatagtgtatcaaattttgttgtgaagttggatgcttgatgtgcttaatttgtttttccgatggtgattgtagGATTCTGACTTGGAGAAGGCCCAGCTTGGCCTGGGGCATAGCTACAGCAGGGCCAAGGTGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaa--ttaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
           ||| | |||||       | |  || ||  | | |||| |  | |||    |   |   |   |  || ||| | |  | | | | ||||  |  ||  |||||     || |||||||  |||||||||| |||||||||||||| || |||||||||||||||||||||||||| ||||| ||| | || || || ||||| ||||| |
----------gttagtgtttcctcatgcctctttttgtgtttctgtgtgcaggataactgtgtcctatttttatcactaatttatatata-tattttttatgctgcttgattttc---acagTCTGGAGATTTAGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAGTTTAATGTTAACCGTGTTGACAACATGGTTATTCAAG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
------gtttgctt-tatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
       ||| ||  |   |  | | |   |  | |          || | |||| ||  |  | | ||     ||      |||||| |||  | | | | || |    || |||      ||||| | || ||  | |||||||| |||||||||||||| || ||||||||||||||||||||||| |||||||| ||| | || || || ||||||||||| |
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagt------tattttatttaaattatttttttt--ccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcg-gtattttctttgca-atttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
           ||| | |||||    |    | ||| ||  ||| ||| |   |  |||  |  |   ||      |   |  |||  | |||  | || |  |  ||  |||| |    || |||||||  | |||||||| ||||||||||||||||| ||||||||||| |||||||||||||| ||||| ||| | || || || ||||| ||||| |
----------gttagtgtttcctc--atgcctccttttgtgtttctgtat-ccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttc--acagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaattt-ctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
                             | || |      | | ||||| | | | |  ||     ||  ||  ||| |  | ||   | |  ||| |||  |  | | | |   |||||||||| || || |||||  | || |||||  | |  ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||| ||||| |
----------------------------gtgtgatctcctttctatgtgtttaaaatctttttgtctgtttgct-tatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
                                     ||  ||||| | | ||  |  |  |||    ||  |  ||||||   |     | |||  |||  || |  |||    |||||||||| ||  | ||||| || |||||||| || |  || || ||||||||||||||||||||||||||||| ||| | || ||||| ||||| ||||| |
------------------------------------gtgtgttttt-tatttttgattacctaatacctacaca-tatttttgctattcgtgctca-atatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG

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|71864289|gb|DT013344.1|DT013344
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|110712950|gb|EE088442.1|EE088442
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|110686032|gb|EE063274.1|EE063274
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|71861748|gb|DT010803.1|DT010803
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|110690304|gb|EE067284.1|EE067284
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|110718517|gb|EE095438.1|EE095438
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|71865133|gb|DT014188.1|DT014188
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|161719328|gb|FC068961.1|FC068961
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|33404147|gb|CF209774.1|CF209774
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|110701410|gb|EE078950.1|EE078950
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|161720525|gb|FC070912.1|FC070912
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
EST: gi|71857394|gb|DT006449.1|DT006449
EST:     TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAG                         CCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA
genomic: TTCTCCGTGGTGTGCGGTTGCATTTTGATAGGTTTATTAAGGATCTCAAGgtttgcttta ... ttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
                                    tatttatttttcctt  CT-rich tract
                      aatttctcttatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG

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