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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactaaaatcaataccgaatgttctgatttccttcttgtttcatggtcctgatacttgtttttgaatgtttcttcctcgtactttttgcctgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG

Basic information

species Vitis vinifera
transcript Vv08s0040g02540.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 3'ss of exon 8
aactaaaatcaataccgaatgttctgatttccttcttgtttcatggtcctgatacttgtttttgaatgtttcttcctcgtactttttgcctgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG
   |    |    || |  ||| ||  |   ||     ||||||     |  ||| | | | |   | | | |   | |     |||   || || | |||  ||    || ||| ||||||| || ||| |||| || || ||||||||||| ||||||||| | ||||||||||| || || |||   || || || |
gtttgtcctttcaactgtttgtactt-tgcactgtcaatttcatctctattgtacct-tatatccttatctgtagttggccacattttgttgggatacagAAATGTGTAGTTGATTTGCCTGGTGGACCATTGGAAATCGAATGGAGGGAGGATGACAATCATATTTACATGACTGGTCCTGCAGAGGCTGTCTTCTATG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AC182617.3_FGT001 (Zea mays), 3'ss of exon 8
------------aactaaaatcaataccgaatgttctg--atttccttcttgtttcatggtcctgatactt----gtttttga-atgtttcttcctcgtactttttgcctgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG
              |     |   |      | || ||  |||||  || || |||||  ||   ||| ||    |||||||  ||   |  | ||   |||||||  |  ||||| |||  ||    || ||| ||||||| |||||| |||| ||||||||||||||||| ||||||||||| ||||||||||| || || ||| |||| ||||| |
gtttgtcattctttcctttctgtgtgtttgctattttggcatttcactcatgattcatattcactatagtttatagtttttgttataccttattctttaactttttatc-atgaaacagAAATGTGTAGTTGATTTGCCTGGCGGGCCATTGGAAATTGAGTGGAGGGAGGATGACAATCATGTTTACATGACTGGTCCTGCAGAGGTCGTCTTTTATG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G130332_T03 (Zea mays), 3'ss of exon 8
---------aactaaaatcaataccgaatgttctg--atttccttcttgtttcatggtcctgatacttgtttttgaatgtttcttcctcgtactttttgcctgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG
            |    |   |      | || ||  |||||  || | |||  |       ||| ||  | ||  |  ||  |   |  |  ||||   |     || |||  ||    || ||| ||||||| |||||| |||| ||||||||||||||||| ||||||||||| ||||||||||| || || |||  ||| ||||| |
gtttgtctttcttgccttttgtgtttgcttttttggcatttcactcatatttactacagtctatagtttgtgttataccttgatcttttatttttttaatc---ataacagAAATGTGTAGTTGATTTGCCTGGCGGGCCATTGGAAATTGAGTGGAGGGAGGATGACAATCATGTTTACATGACTGGTCCTGCAGAGGCCGTCTTTTATG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G35780.1 (Glycine max), 3'ss of exon 8
aactaaaatcaataccgaatgttctgat--ttccttcttgtttcatggtcctgatacttgtttttgaatgtttcttcctcgtactttttgcctgt------gaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG
            |   || |  |    |  ||||| | |||| ||        | |    | |  |    |||   | |  |  ||||   ||||      || | ||| |||||| || ||||| ||||||||||| ||  | |||||||||||||||||||| |||||||| || ||||| ||| |||| ||  | || | ||| |
--------atgcttttgattagttaagtgcttcctccctgttccaaaaaaaaaaaaaaactgtacgttgattttgccataatttttttaatctgtcaatttgatacagAATTGCACGGTTGATCTACCTGGAGGGCCTCTTCAGATTGAGTGGAGGGAGGAAGATAATCATGTTTATATGACAGGCTCAGCCGATGTAGTTTATTATG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G33080.1 (Glycine max), 3'ss of exon 9
aactaaaatcaataccgaatgttctgatttccttcttgtttcatggtcctgat-acttgtttttgaatgtttcttcc-tcgtactttttgcctgt------gaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG
        | | |   |  |    |  ||   | |||  | |||| |||  |  | ||| | |    || || | || |  |  ||||   ||||      || | ||| |||||| || ||||| |||||||| || ||  | ||||| |||||||||||||| |||||||| || ||||| ||| |||| ||  | || | |||||
--------ttatttttgctttggttagttaagtgcttcctccatgttcccaaagaattgctgtacgttgattttgccataatttttttaatctgtcaatttgatacagAATTGCACGGTTGATCTACCTGGAGGACCTCTTCAGATTGAATGGAGGGAGGAAGATAATCATGTTTATATGACAGGCTCAGCCGATGTAGTTTATTACG

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|110423566|gb|EC989913.1|EC989913
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AATTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|71868419|gb|DT017474.1|DT017474
EST:     GTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|110379227|gb|EC944409.1|EC944409
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|110363795|gb|EC927411.1|EC927411
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|34549331|gb|CF517563.1|CF517563
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|32458996|gb|CD800170.1|CD800170
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|110382285|gb|EC939068.1|EC939068
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|110728275|gb|EE103711.1|EE103711
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|110717263|gb|EE092967.1|EE092967
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|34549417|gb|CF517649.1|CF517649
EST:     TGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: TGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
EST: gi|110423955|gb|EC990308.1|EC990308
EST:     GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG                         AGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG
genomic: GAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcc ... tgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctgatacttgtttttgaatgtttcttcctcgtactttttgcctgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG
 tcctgat  putative branch site (score: 3)
                       tttcttcctcgtactt  putative PPT
             tttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactaaaatcaataccgaatgttctgatttccttcttgtttcatggtcctgatacttgtttttgaatgtttcttcctcgtactttttgcctgtgaaatagAGTTGCACCGTGGATCTGCCTGGAGGGCCACTGGATATTGAGTGGAGGGAGGAAGACAATCATGTGTACATGACTGGCCCAGCTGAGATCGTGTTTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - -aaatcaa
- - - - - - - ccgaatg
- - - - - - - - - - - - - - -tccttct
- - - - - - - - - - - - - - - - - - - - -catggtc
- - - - - - - - - - - - - - - - - - - - - - - - ctgatac