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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGTCAAGACCGTGCCGCGTCATCACCACCCTCACGCTCCTCCTGATAACTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctcttctctctctctctctctctctctctcttttttcttttttctttttacattttccattatttgatttccagatctacaatcactgctttcc...

Basic information

species Vitis vinifera
transcript Vv12s0035g02180.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os03g52630.1 (Oryza sativa), 5'ss of exon 1
ATCGTCAAGACCGTGCCGCGTCATCACCACCCTCACGCTCCTCCTGATAACTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctcttctctctctctctctctctctctctcttttttcttttttctttttacattttccattatttgatttccagatctacaatcactgctttcc-
|||||||||  ||| || |   | | || |||||   |||| || ||  | |||||||  ||||||||||||||||| |||||||||||||| || || |||  || | || || |||  |  ||| |||  ||||  | |   | |   |    | |         |   ||||||   ||  | |  |  |  |   | 
ATCGTCAAGCTCGTCCCCCACAAGCGCCCCCCTCCTCCTCCCCCCGACCAGTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagtttttt-tcactcctttcctccctccgtctccatctctgtctgcatcagaagaagaggaggaagaagatttcagaattcagatccggttttgcacg

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA09G02160.1 (Glycine max), 5'ss of exon 1
ATCGTCAAGACCGTGCCGCGTCATCACCACCCTCACGCTCCTCCTGATAACTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtct-cttctctctctctctctctctctctctcttttttcttttttctttttacattttccattatttgatttccagatctacaatcactgctttcc
|||||||| ||||| || || || | ||||   ||| | ||||| || ||||||||||||||||||||||||||||| ||||||||||| ||||| || |||||||   |  || |     |  |||  || ||| ||     |    | |  | |  ||   | |   ||||  ||       | ||             
ATCGTCAACACCGTCCCCCGCCACCGCCACAAACACCCCCCTCCCGACAACTACACCCTCGCCCTCCACAAGGCCCTCATGTTCTTCAATGCCCAACGATgtatgtaaacaacttttggagtaactcaatccctc-ctccaaccaaaatacagtatgtataaactaacttttgtgttgtgttgttgcag------------

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA15G13080.1 (Glycine max), 5'ss of exon 1
ATCGTCAAGACCGTGCCGCGTCATCACCACCCTCACGCTCCTCCTGATAACTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctcttctctctctctctctctctctctctcttttttcttttttctttttacattttccattatttgatttccag--atctacaatcactgctttcc-
|||||||| ||||| || || || | ||||   ||| | ||||| || ||||||||||||||||||||||||||||| ||||||||||| | ||| || ||||||||   |  |              |   || |   ||   |     |    |||            |||  |  ||  |      ||  |  |  | | 
ATCGTCAACACCGTCCCCCGCCACCGCCACAAACACCCCCCTCCCGACAACTACACCCTCGCCCTCCACAAGGCCCTCATGTTCTTCAATGGCCAACGATgtatgtcaactaccaaataaagaagaagt---tcccgcattgagtaaacataaaaacaagagaggagggatgaagtaaagttactcctcatttccacagttca

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|352774173|gb|FQ474696.1|FQ474696
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|110371632|gb|EC935746.1|EC935746
EST:     TCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: TCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|110685593|gb|EE062450.1|EE062450
EST:     CTACACCCTCGCCCTCCACA-GGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAA-GCATAATAATGTTTTCCTGGAGGGGTAACTCGGGT
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTT-CCTGGAGGGGTAACTCGGGT
EST: gi|352777373|gb|FQ474007.1|FQ474007
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|352769692|gb|FQ468620.1|FQ468620
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCG
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCG
EST: gi|352769682|gb|FQ468610.1|FQ468610
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGG
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGG
EST: gi|352768658|gb|FQ467870.1|FQ467870
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|352764883|gb|FQ471943.1|FQ471943
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGGCATAATAATGTTTCCTGGAGGGGTAACTCGGGT
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAG-CATAATAATGTTTCCTGGAGGGGTAACTCGGGT
EST: gi|352773734|gb|FQ472516.1|FQ472516
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|110685567|gb|EE062410.1|EE062410
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGGTCTTCAACGCCCAGCGGT                         CTGGAAAACTCCCAA-GCATAATA-TGGTTTC-TGAAGGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATG-TTTCCTGGAGGGGTA
EST: gi|352776645|gb|FQ465443.1|FQ465443
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|110700071|gb|EE077691.1|EE077691
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|352773818|gb|FQ472600.1|FQ472600
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACCCCCAGCGTT                         CTGGAAAACTCCCAAAG
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAG
EST: gi|110719700|gb|EE095055.1|EE095055
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
EST: gi|161707094|gb|FC055557.1|FC055557
EST:     CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTT                         CTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA
genomic: CTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctct ... atatttgcagCTGGAAAACTCCCAAAGCATAATAATGTTTCCTGGAGGGGTAACTCGGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGTCAAGACCGTGCCGCGTCATCACCACCCTCACGCTCCTCCTGATAACTACACCCTCGCCCTCCACAAGGCCCTTATGTTCTTCAACGCCCAGCGTTgtatgtctcttctctctctctctctctctctctctcttttttcttttttctttttacattttccattatttgatttccagatctacaatcactgctttcc

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