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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattatggaaattgtctggatttgaaattaggtggtttttatcttatggatgaactgaatttcgttttctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGATCGTGGATAGTATTCATCATCAAGTATCAAAGATCGAGGATGATCTTAAG

Basic information

species Vitis vinifera
transcript Vv14s0068g01280.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 3
----------------gtgattatggaaattgtctgg--atttgaaattaggtggtttttatcttatggatgaactgaatttcgttttctaatgga--agATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGATCGTGGATAGTATTCATCATCAAGTATCAAAGATCGAGGATGATCTTAAG
                    ||    ||  ||  |||  | ||     |   |    |  |    ||  ||  |     |||  |||| || |||   || ||||||||||| || || ||||  || || ||||| ||| ||| ||||||||||||| |||||||   ||||||  ||||||||||||||||||| |||
ttgccgatcactaatttccgttggaaaacctgattggctactttggtgtgtctcccctccaagccatttatttatctgttttttttttttattggtccagGTTTGTTTGGGATGAGGCAAAGTACCCGACCATGTCGCCTTTGAAGGAGATCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAG
















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|351031454|gb|FQ446657.1|FQ446657
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|349830231|gb|FQ420491.1|FQ420491
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCGCCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|351024893|gb|FQ433310.1|FQ433310
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCACACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|71881861|gb|DT030916.1|DT030916
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|110699022|gb|EE077184.1|EE077184
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|110693329|gb|EE069475.1|EE069475
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|349833078|gb|FQ416456.1|FQ416456
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|71882447|gb|DT031502.1|DT031502
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|27581998|gb|CB004693.1|CB004693
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|161716182|gb|FC069494.1|FC069494
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|71883798|gb|DT032853.1|DT032853
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|71858149|gb|DT007204.1|DT007204
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|351020303|gb|FQ445910.1|FQ445910
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|71887796|gb|DT036851.1|DT036851
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|110693330|gb|EE069469.1|EE069469
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|110700866|gb|EE077894.1|EE077894
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|294964114|gb|GW837917.1|GW837917
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGACACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
EST: gi|349830278|gb|FQ420538.1|FQ420538
EST:     ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCGCCAG                         ATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT
genomic: ACAAGTGCACTTACGGTGGATGGAGTACCAGTTGATTCCTACCTCACCAGgtgattatgg ... ctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattaggtggtttttatcttatggatgaactgaatttcgttttctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGATCGTGGATAGTATTCATCATCAAGTATCAAAGATCGAGGATGATCTTAAG
                                           ttctaat  putative branch site (score: 2)
                                    tttcgttttct  CT-rich tract
            tttttatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattatggaaattgtctggatttgaaattaggtggtttttatcttatggatgaactgaatttcgttttctaatggaagATTTGTTTGGGACGAAGCCAAGTTTCCCACGATGTCACCTCTGAGGGAGATCGTGGATAGTATTCATCATCAAGTATCAAAGATCGAGGATGATCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG