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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctcagattttgggtttttttttttttttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt...

Basic information

species Vitis vinifera
transcript Vv15s0046g00140.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 5'ss of exon 1
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgta-tgttgtttttcttttgatttctctcagattttgggtttttttttttttttgtttttttgttgagttttcaagtgtgttt---cggttatttgatgatttt
|||||||  ||| ||||||||| | |||||||| || |||||| ||||||||||| | || |||||||| ||||| ||||||||||||||||||||   |||| |  |      |||  |     ||    |||        ||    |  |     |  | ||    |||   ||||    |   || ||  ||  | |    
CTACATCTGCATCCTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTCGGCTGCACGCCCGGCATGGCCTGGACCGTCGTCAATCTCTTCCACTTCGCGgtaatcctccccgccttgcgccacgtcctccattcattaccattcccgtcgtcatcgtcgtcgtccgttttgtgagtgccactacgcgcttgctttgtaa----

upper sequence: Vv15s0046g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 1
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctc-agattttgggtttttttttttt-tttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt
|||||||||||| ||||||||| | ||||| || || |||||| ||||||||||| | || ||||||||||||||  ||||||| |||  ||||||   |||| |      | ||| |   ||||| |  || || || ||    |         |  || |||   |||||       |   ||| |  | | || |    
CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccctccttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagtttagctcgctcgctcgttcgtatcatcagg--

upper sequence: Vv15s0046g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctcagattttgggtttttttttttttttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt--
|||||||||| | ||||||||||| ||||| || || |||||| ||| || |||||| || || || |||||||| |||||||| |||  ||||||    ||| ||      ||          ||    ||       |   ||  ||    |    |||| |   | ||  | |    | || |   ||  |||||    
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctccttctttcattag--tccgatccgttcttgattagcg

upper sequence: Vv15s0046g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G114911_T02 (Zea mays), 5'ss of exon 1
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctcagattttgggttttttttttt-ttttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt--
||||||||||||| |||||||| | |||||||| || |||||| ||||||||||| | |||||||  |||||||| |||||||| |||||||||||   ||||    |  |  |||  | |   || ||  |     |  |    |      | || | |  ||   |  |||   | || | | |   | |||   |     
CTACATCCTCATTGTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTCGGCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgta-accgcct--cttccgttccttcccaagtcccaagcctcccctcccgcctcgtatgtgcgtgcggggttcccatttgctgctgaattgtgaccctgggtg

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|33408811|gb|CF214438.1|CF214438
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110717773|gb|EE093925.1|EE093925
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|22013006|gb|BQ798040.1|BQ798040
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110379719|gb|EC944937.1|EC944937
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110408974|gb|EC974627.1|EC974627
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110705855|gb|EE083181.1|EE083181
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110396783|gb|EC962483.1|EC962483
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|351053778|gb|FQ441544.1|FQ441544
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110380098|gb|EC945340.1|EC945340
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110702334|gb|EE080930.1|EE080930
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110385627|gb|EC950171.1|EC950171
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110373660|gb|EC937916.1|EC937916
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110706167|gb|EE083842.1|EE083842
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|30321089|gb|CD004351.1|CD004351
EST:     TCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: TCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110398590|gb|EC965059.1|EC965059
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|18458776|gb|BM437054.1|BM437054
EST:     TCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: TCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110728899|gb|EE104881.1|EE104881
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110388187|gb|EC952911.1|EC952911
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|22013007|gb|BQ798041.1|BQ798041
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110371796|gb|EC935920.1|EC935920
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|30320507|gb|CD003769.1|CD003769
EST:     TCCACTTTTTG                         GTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: TCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
EST: gi|110715253|gb|EE093094.1|EE093094
EST:     GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTG                         GTCACATATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC
genomic: GCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtt ... cacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctcagattttgggtttttttttttttttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttctctc