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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgaaatcaatcctgaccattagttggccctttgcattatataatactttaaatggatcagatcttgtgtatgttcaagaatttctcctctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAACATACTGTTCCAAATGTTTTTATTG

Basic information

species Vitis vinifera
transcript Vv07s0005g04860.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G04770.1 (Glycine max), 3'ss of exon 1
tcatgaaatcaatcctgaccattagttggcccttt---gcattatataatactttaaatggatcagatcttgt-gtatgttca---agaatttctcctctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAACATACTGTTCCAAATGTTTTTATTG
       |||  || |||   |||||||   ||||   | | ||||| |      ||||   ||    ||| |  | |||| |    |  | | || |   | | ||| || |||||||||||| ||||||||||  |||||||| | || || ||||| ||||| |||||||| |||||||
-------atctctcttgatgtttagttgttgctttatggtactatattaagggggaaatcattctacacttatcatttgtttatttggtttgtatcttaaatgttagGTCCTCAAGGGCCACAGTTGCAGAAGGTATTGGAAAGGATCACAGGGCAACACACTGTGCCAAATGTATTTATTG

upper sequence: Vv07s0005g04860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G04770.2 (Glycine max), 3'ss of exon 1
tcatgaaatcaatcctgaccattagttggccctttgcattatataatactttaaatggatcagatcttgt-gtatgttca---agaatttctcctctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAACATACTGTTCCAAATGTTTTTATTG
               ||   | | ||||     | | | ||||| |      ||||   ||    ||| |  | |||| |    |  | | || |   | | ||| || |||||||||||| ||||||||||  |||||||| | || || ||||| ||||| |||||||| |||||||
-------------gatgtttagttgttgctttatggtactatattaagggggaaatcattctacacttatcatttgtttatttggtttgtatcttaaatgttaggtcctcaagGGCCACAGTTGCAGAAGGTATTGGAAAGGATCACAGGGCAACACACTGTGCCAAATGTATTTATTG

upper sequence: Vv07s0005g04860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G28730.1 (Arabidopsis thaliana), 3'ss of exon 2
tcatgaaatcaatcctgaccattagttggccctttgcattatataatacttta----aatggatcagatcttgtgtatg-ttcaagaatttctcctctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAACATACTGTTCCAAATGTTTTTATTG
   || |||     |  |   || | ||    |   ||  | | |||  |||       |  |||  |  || ||| ||  | ||  || | |  |   ||||||| || ||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||||| ||||||||  |  
---tgcaattg--tcaaaatgtttggtgattttggacaacaaagaatgatttgttatgttctatctaaagttctgtttgactaaactatgtttggttaatttcagGTCCACAAGGGCCACAACTGCAGAAGGTACTGGAAAGACTTACTGGGCAACACACTGTTCCTAATGTTTTCGTAT

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|110359775|gb|EC921888.1|EC921888
EST:     GTTCAAGCGACTTGGTGTAGAACCTTTTGTGATTGAATTGGACGAGATGG                         GACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAAC
genomic: GTTCAAGCGACTTGGTGTAGAACCTTTTGTGATTGAATTGGACGAGATGGgtgagtattc ... tctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAAC
EST: gi|46910003|gb|CN545378.1|CN545378
EST:     GTTCAAGCGACTTGGTGTAGAACCTTTTGTGATTGAATTGGACGAGATGG                         GTCCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAAC
genomic: GTTCAAGCGACTTGGTGTAGAACCTTTTGTGATTGAATTGGACGAGATGGgtgagtattc ... tctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAAC
EST: gi|51050807|gb|CO818738.1|CO818738
EST:     GTTCAAGCGACTTGGTGTAGAACCTTTTGTGATTGAATTGGACGAGATGG                         GTCCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAAC
genomic: GTTCAAGCGACTTGGTGTAGAACCTTTTGTGATTGAATTGGACGAGATGGgtgagtattc ... tctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactttaaatggatcagatcttgtgtatgttcaagaatttctcctctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAACATACTGTTCCAAATGTTTTTATTG
                                      tttctcctctctttc  CT-rich tract
                                 aagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgaaatcaatcctgaccattagttggccctttgcattatataatactttaaatggatcagatcttgtgtatgttcaagaatttctcctctctttcagGACCCCAAGGGCCACAGCTGCAGAAGGTGCTGGAAAGGCTTACTGGACAACATACTGTTCCAAATGTTTTTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - -aaatcaa
- - - - - - -cctgacc
- - - - - - - - - - - tagttgg
- - - - - - - - - - - - - - - cctttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - aaatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaagaa