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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaagaaatgctgtgttacgaatgcacacattctatctccttgtttaattataagaatgctagcagcttatacatgtgatagtctcaatttttggggttttttaaactgcatttagctttagtttctaagttgcttccataacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGGGGGCTTTCCTTTCAAAGGGATACCGTGACAAGAGGAGGCTG

Basic information

species Vitis vinifera
transcript Vv08s0040g03130.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g03130.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g17600.1 (Oryza sativa), 3'ss of exon 6
gtacttaagaaatgctgtgttacgaatgcacacattctatctccttgtttaattataagaatgctagcagcttatacatgtgatagtctcaatttttggggttttttaaactgcatttagctttagtttctaagttgcttccataacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGGGGGCTTTCCTTTCAAAGGGATACCGTGACAAGAGGAGGCTG
                                                                  | | ||  |||  |  | | |  | || ||  |   ||| |   |  |    |    ||  |    || ||  |||| |        ||| ||||| ||||||||||| |||||||||||||| ||  | ||||| ||||  || || ||  | | |   |||   || | ||| || ||
------------------------------------------------------------------gtaactcctactggataaatttcccatcttgtgtagtttctgctcctcgacaaa---tacataaatagctgtatccaca--------gGCCGGTTTGAAGATTATACAGTTGTACATGGAAGGATACAGGCAGGATTGGGAACTGTCGTTCGAGAAGACCACCAGAACGAAAGGTGGATG
















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|26263854|gb|CA814917.1|CA814917
EST:     ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAG                         GCAGGTTTAAAGATTATACAGTTGTACATGGAAGGTTATCGACAGGACTGG
genomic: ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAGgtacttaaga ... aacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG
EST: gi|110374235|gb|EC938881.1|EC938881
EST:     ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAG                         GCAGGTTTAAAGATTATACAGTTGTACATGGAAGGTTATCGACAGGACTGG
genomic: ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAGgtacttaaga ... aacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG
EST: gi|110731056|gb|EE108844.1|EE108844
EST:     ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAG                         GCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG
genomic: ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAGgtacttaaga ... aacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG
EST: gi|351021722|gb|FQ437107.1|FQ437107
EST:     TGAAGTACTGGGATTTGTTTCTGGAGTTTTTAAGCACATTTACTCCCCAG                         GCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG
genomic: TGAAGTACTGGGATTTGTTTCTGGAGTTTT-AAGCACATTTACTCCCCAGgtacttaaga ... aacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG
EST: gi|110360893|gb|EC924336.1|EC924336
EST:     ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAG                         GCAGGTTTAAAGATTATACAGTTGTACATGGAAGGTTATCGACAGGACTGG
genomic: ATGAAGTACTGGGATTTGTTTCTGGAGTTTTAAGCACATTTACTCCCCAGgtacttaaga ... aacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttttaaactgcatttagctttagtttctaagttgcttccataacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGGGGGCTTTCCTTTCAAAGGGATACCGTGACAAGAGGAGGCTG
                                         ccataac  putative branch site (score: 3)
                                           ataacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaagaaatgctgtgttacgaatgcacacattctatctccttgtttaattataagaatgctagcagcttatacatgtgatagtctcaatttttggggttttttaaactgcatttagctttagtttctaagttgcttccataacattttagGCAGGTTTAAAGATTATACAATTGTACATGGAAGGTTATCGACAGGACTGGGGGCTTTCCTTTCAAAGGGATACCGTGACAAGAGGAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG