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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacatttttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG

Basic information

species Vitis vinifera
transcript Vv08s0007g08110.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacattt--ttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
                | | | ||       |    ||||| |     |     |  |   | |  |   |  |   || | |||   |||   ||| || |   | | |||  |||||||||| ||||||||  | |||||||| ||  ||||||| |||||||||||| |||||||| | ||||| |||
---------------gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataa-tttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacatttttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
|||||         |  ||||   | |||||| || |  ||| |        ||     ||||| |  |   |  ||||| |   ||   || |||        || |||| |||||||||| ||||| ||| | ||||| || |||||||||||||||||||||||||||||||||||||| ||||||
gtaagtctcttg--tactatgcatttagtgctaggctcacccccctccccccaa-----ttttcgttcg---tcttgaattctgattc--tgtcta--------gaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G12560.2 (Glycine max), 3'ss of exon 3
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacatttttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
|||||         |  |||    | |||||| || |  ||| | |       ||       || | |  | | |||| |          || |||        || |||| |||||||||| ||||| ||| |||| || || |||||||||||||||||||||||||||||||||||||| ||||||
gtaagtctcttg--tactattcatttagtgctaggctcaccccccatccccccaattctcgctcttcttgaattctgatt---------ctgtcta--------gaattttccagGTAAAGAGCATGCTCTTGTTATCTCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G32420.1 (Glycine max), 3'ss of exon 3
---------------------------------------gtaaggtcaaaaa-cttttatgggctgagtgc-tgggttttccctcaaaggaggaaa----gatattttcctgtg-cagtgctgaatacatttttattggctaatgttggtgagt-ttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
                                        ||    |   |  ||||  || | ||      |    ||  | || |   ||||||    |  |  ||| || | ||    |   |    | | ||    |  |  || |  || || ||||||||||| ||||||||| | |||   || ||||||||||| |||||||||||||||||||||||||  ||||||
gtaagtcttttgttagcctatgatttagcactaagcactttactccctccattctttcgtgtgttgtacatgtattcttatcttctagaaaggaaaaggggggaggttcttgggacaacatttgcttacatataataatttggttctgttttgtattatcagGTAAAGAGCATGCACTTGTGATAAGCAATCACAGAAGTGATATTGATTGGCTTGTTGGATGGGTTTCAGCTCAG

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 3
-----------------------------------------gtaaggtcaaaaactttt--atgggctgagtgctgggttttccctc----aaaggaggaaagatattttcctgtg-cagtgctgaatacatttttattggctaatgttggtgagtttt-tcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
                                               || |    || |  ||| | || ||      | ||  ||     ||||||  |  |  |  ||| || | ||    |   | |  | | ||    | ||  || |  || || ||||||||||| ||||||||| | |||   || ||||||||||| |||||||||||||||||||||||||  ||||||
gtaagccttttgttagcctatgatttagcactaagcaatttactccctccattctttctccatgtgttgtgtatgcattcttatcttctagaaaggaaaagggggaggttcttgggacaacatttgcttccatataataatttgattctgttttgtattatcagGTAAAGAGCATGCACTTGTGATAAGCAATCACAGAAGTGATATTGATTGGCTTGTTGGATGGGTTTCAGCTCAG

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaat--acatttttattggctaatgttggtgagtttttc-agGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
||||| ||| |  |||  || |||       |  ||||    |      | || | | | || ||| || |     ||||    |  || |||| ||  |  |  |   |||||| ||| ||||||||||| ||| |  | |  || ||| ||||||| |||||||||||||| |||||| || ||||||||
gtaagttcatatgctt--attggcaatcaaatcagtttctgatgtcttcaagatataaaatt-cctatgtaagaacgaatctgtaacttcattgactg-tcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG

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|110685332|gb|EE063631.1|EE063631
EST:     ATCCAACTGTACACAGATCCAGAAACATTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|30252575|gb|CB970126.1|CB970126
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|71862495|gb|DT011550.1|DT011550
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|71864165|gb|DT013220.1|DT013220
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|161706024|gb|FC056715.1|FC056715
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|71866396|gb|DT015451.1|DT015451
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|71874295|gb|DT023350.1|DT023350
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|161717359|gb|FC065274.1|FC065274
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|33405255|gb|CF210882.1|CF210882
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|110696361|gb|EE072411.1|EE072411
EST:     ATCCAACTGTACACAGATCCAGAAACATTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|110708022|gb|EE085087.1|EE085087
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|161715416|gb|FC068047.1|FC068047
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
EST: gi|77578022|gb|DV217773.1|DV217773
EST:     ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG                         GTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC
genomic: ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGGgtaaggtcaa ... agtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctgtgcagtgctgaatacatttttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
                               ggctaat  putative branch site (score: 3)
                                               tttttc  putative PPT
               tgaatacatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacatttttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT