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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtattgtctttgcagacgtcttattgttctctctgtcttatatgcctaattattttctgaacag

Basic information

species Vitis vinifera
transcript Vv04s0044g01480.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G088974_T01 (Zea mays), 5'ss of exon 6
GTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgt-actgtattgtctttgcagacgtcttattgttctctctgtc--ttatatgcctaattattttctgaacag--------
 |   |||  || |||   | || || |  || || |||||||||||||| ||||||||| ||||||| |||| ||| ||  |||||||||| ||| ||||   |   |  |  |      | | |  | | | ||||| |   ||||||   | | |  ||| |    |         
ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtccttaattatcattttcttatcctagatatctctattaattatataagtgaatcctttgttcttatgtaattag

upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 6
GTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactg-tatt-gtctttgcagacgtcttattgttctctctgtcttatatgcctaattattttctgaacag---------------------------------------------------
||||||||| | |  ||||| ||||| |||||||||||||| |||||||| |||||||||||||||||    |||||||| ||||||||||| ||| | ||| |  | || |   | | ||    | ||||  ||  | |   |  | |   || || || | | | |                                                     
GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacag

upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G26250.1 (Glycine max), 5'ss of exon 6
GTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtattgtctttgcagacgtcttattgttctctctgtct-tatatgcctaattattttctgaacag---------------------------------------------------
||||||||| | |  ||||| || || |||||||||||||| || ||||| |||||||||||||||||   ||||||||| |||||||| || ||| | |||  ||| ||| | |  ||    |  ||| |||  | |   | ||| |   || || ||   | | |                                                     
GTGCATGTCTGTGATATTGATAATCCAGAGGAAGCATCATTTTTCGAATCTTTTGAAGCAGCACACTCCTTGCATGACTTATCTAGCTCAATCGCAGAAgta--gtactgtttctatagttaacacatttttccttattcatatatttttttagtttttcatttagctcttttagatttaatctgcagacatttcttgaccattattacttcatgaacag

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|351054641|gb|FQ456838.1|FQ456838
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCCAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351038015|gb|FQ460757.1|FQ460757
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351042217|gb|FQ442684.1|FQ442684
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|349828516|gb|FQ417258.1|FQ417258
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351057082|gb|FQ450789.1|FQ450789
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCANAG                         AAACTTGGAGTCGAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351056977|gb|FQ443604.1|FQ443604
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCCAAG                         AAACTTGGAGTCCAAGCACCCCCAGTTAGAATTGATAGCCAGGCCAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351039598|gb|FQ461465.1|FQ461465
EST:     CATTTGAGGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|349825261|gb|FQ417982.1|FQ417982
EST:     CATTTGAAGCAGCACACTCAAGGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|352794444|gb|FQ481676.1|FQ481676
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|122689385|gb|EC938204.1|EC938204
EST:     CATTCGAAGCAGCACACTCAAAGCATGACTTGTCTAGTTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCAAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|122688865|gb|EC927133.1|EC927133
EST:     CATTCGAAGCAGCACACTCAAAGCATGACTTGTCTAGTTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCAAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351038675|gb|FQ464541.1|FQ464541
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|352793784|gb|FQ481938.1|FQ481938
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|161709570|gb|FC061400.1|FC061400
EST:     CATTCGAAGCAGCACACTCAAAGCATGACTTGTCTAGTTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCAAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351017111|gb|FQ424538.1|FQ424538
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
EST: gi|351042941|gb|FQ451235.1|FQ451235
EST:     CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG                         AAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT
genomic: CATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtatt ... ttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgtactgtattgtctttgcagacgtcttattgttctctctgtcttatatgcctaattattttctgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG