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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattgatgaaagtttttaactacttttttacaggaactccctgatgattgtaagaagcagatatggttaatttttcttctgataattgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCTACAACCAATCTGGCAATGGCCGGCCGGACTATTCGCTGGACCAGTCATA

Basic information

species Vitis vinifera
transcript Vv04s0023g02570.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02570.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G37630.1 (Glycine max), 3'ss of exon 3
gtaaaattga---tgaaagtttttaactacttttttacaggaac--tccctgatgattgtaagaagcagatatggttaatttttcttctgataattgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCTACAACCAATCTGGCAATGGCCGGCCGGACTATTCGCTGGACCAGTCATA
 | ||||      || |   | | | |     ||| | ||   |  |   || |  ||  |||  |||  |   |   |       | || ||||    |  |||||||||||| || || |||||||| ||||| |||||||| || || || ||||||||| | ||||||||     | ||||   | || || ||    ||
-tgaaatcccatttggactatatcagcgtgcgtttgatagtttcaattattggtattttaaagctgcatttccagcataaacaatatttg-taat--gttatagGGAGCCACACTATAGGAAATTCCCGATGCACCAGCTTCAGGCAAAGACTATACAACCAAACAGGCAATGGAAAAGCAGACTTCACTCTTGATCAAGTGTA

upper sequence: Vv04s0023g02570.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G07670.1 (Glycine max), 3'ss of exon 3
gtaaaattgatgaaagtttttaactactt--ttttacaggaactccctgatgattgtaagaagcagatatggttaattt----ttcttctgataatt--gagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCTACAACCAATCTGGCAATGGCCGGCCGGACTATTCGCTGGACCAGTCATA
       | |    ||||||| || |  |  |   |    |  | |    |  |||| | |  |   |  |  || |||    | | | ||||| ||   | |  |||||||||||| || || |||||||| ||||| |||||||| || || || ||||||||| | || |||||     | ||||   | || || ||    ||
-------taaaatgagtttttgacaaaatagtacaatcaaacatgctattttgttgtgaaatcccatttggactattttaacgtgcgtttgatactttcaattatagGGAGCCACACTATAGGAAATTCCCGATGCACCAGCTTCAGGCAAAGACTATACAACCAAACAGGAAATGGAAAAGCAGACTTCACTCTTGATCAAGTGTA
















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|351041142|gb|FQ444119.1|FQ444119
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|110363385|gb|EC926968.1|EC926968
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|349830006|gb|FQ420266.1|FQ420266
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|110378383|gb|EC943513.1|EC943513
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|71876626|gb|DT025681.1|DT025681
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTC
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTC
EST: gi|351025527|gb|FQ435220.1|FQ435220
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|110688973|gb|EE068133.1|EE068133
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|349828105|gb|FQ415433.1|FQ415433
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
EST: gi|349828106|gb|FQ415434.1|FQ415434
EST:     CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTG                         GGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT
genomic: CAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattga ... ttgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgattgtaagaagcagatatggttaatttttcttctgataattgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCTACAACCAATCTGGCAATGGCCGGCCGGACTATTCGCTGGACCAGTCATA
                                    ttctgat  putative branch site (score: 3)
                          ttaatttttcttctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattgatgaaagtttttaactacttttttacaggaactccctgatgattgtaagaagcagatatggttaatttttcttctgataattgagtgcagGGAGCCACACAATTGGGAATTCCCGGTGCACAAGCTTCAGACAGAGGCTCTACAACCAATCTGGCAATGGCCGGCCGGACTATTCGCTGGACCAGTCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA