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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta...

Basic information

species Vitis vinifera
transcript Vv03s0038g03120.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtt----tggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
|||| |  | || || ||||| ||  | ||||||||||| |||||||||||| | |||||||||||||||||||| || ||||| || || ||||||||||||  |    ||    | | |||  |   | || || ||   ||         ||  |  | |   |  |  |       | | ||    |||||| ||     
GCACGACAACGTCGACATTGTCGTCATCAGGGAGAACACCGAGGGCGAGTACTCCGGGCTTGAGCACGAGGTCGTCCCTGGCGTCGTGGAGAGCCTTAAGgtatggcgaattccgcttgctgctaactcacctagttga-tgtagtgtttgccagggtgcttgggttaatgcgtgtgccgagagaaccccaaatgcaactt---

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggtt--ctgttttggtaagaaaaaaaatataaaatgcgaccccta
|||| | || || || || || ||  | ||||||||||| ||||| |||||| | ||||| |||||||||||||| |||||||| ||||| ||||| ||||||  | |   |     |    | |  ||  ||     |    |    | |  |   |  |  |       | |   |     |  |  |||| |  || | 
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctt-tgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt-

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaa-atgcgaccccta-
|||| | | ||| || || || ||  | ||||||||||| |||||||||||| | ||||| |||||||||||||| ||||| || || || ||||| ||||||    | |  ||   |    |       | |   |||     |  ||    |||  | | |||| |  |          ||||||  ||  ||| ||   
GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtacta-cggagtgtcggttggggtcggctgcgtttcatgttt-attatgatttttccgatatgttatactccctccttttatataagtatatgacaccgtt

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtt---tggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
|||| |  | || || || || ||  |  |||||||||  |||||||||||| | ||||| ||||| ||||||||||| ||||| || || || || ||||||  |    ||   || ||  ||  | || |  |  ||   |         |  ||    |  | | |    |  | | |    || ||  ||| |  | ||
GCACGACAACGTGGACATCGTCGTCATTCGGGAGAACAGTGAGGGCGAGTACTCGGGGCTCGAGCATGAGGTCGTTCCTGGCGTCGTGGAGAGTCTCAAGgtatggagaattccatgtattgctctacaagtaat--aatgcagtgtgtggcacgctggcaggccagctaatatgtgcatacggcta-aatgtgctaagctta

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
 ||| |  |||||||||| |||||| | || |||||||| || || |||||| | || || ||||| ||||| ||||| || || ||||| |||||||||||||    | | |   |   ||| ||     |  |    |||     ||   ||||||  |   |  || |    ||     | |  |            
ACACGAAAATGTTGATATCGTTGTGATAAGAGAGAACACTGAAGGAGAGTACTCAGGTCTCGAGCATGAGGTTGTTCCTGGTGTTGTCGAGAGCCTTAAGgtaaaccatatataatta--tagggattgtttttagtccaaattgtgatcc-cttttgtatacatgatgttgttgaattgtttgtgtag-----------

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaac-gtctgtttggatgcctagagaactggtggaacataaaagaaaatagactt--ttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
 ||| |  ||||  | || || ||  |  |||||||||| ||||| |||||| |||| ||||| ||||||||||| || || || || || ||||| || ||| |  |||  ||      ||   ||| || |   |  ||       ||  | ||  ||  || | | |    | | | ||  ||  |   || ||  |   
CCACGACAATGTCAACATCGTGGTAATTCGGGAGAACACAGAGGGGGAGTACTCTGGTCTTGAACACGAGGTCGTCCCTGGGGTCGTGGAGAGCCTGAAAgtacctatctcattcacctgcttttgaattgatatgagttatttatttatttatttatttatttatttgtaaacatggacaatgatgcatc-tgtgaatcg--

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgta-acgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
 ||  |  ||||  | ||||| ||  |  ||||||| || || || |||||  |||| ||||||||||||||||| ||||| || ||||| |||||||||||| |  | |  ||   || |  || || |      ||   |          | |  | ||  | ||||  |    ||  |  | |   | ||      | 
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgattgtaatattttc-tgtccaagcatttttttcacgcctttgttt

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaac-gtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
 ||| || ||||  | ||||| ||  |  | |||||||| || || |||||| |||| ||||||||||||||||| ||||| || ||||| ||||| |||||||   |||  ||      |   | || |  |  |  ||  ||       ||  |  ||      ||   ||   |      |||  | |      | | 
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatgcacttttctgcat-

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 5'ss of exon 1
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta
 ||  |  | ||  | ||||||||| |  |||||||||| ||||| |||||||| || || |||||||||||||| || || || |||||    || ||||||   ||   ||   |  |    |   || | |  |     ||    ||   || |  ||  |     |                              
CCATGACAACGTCAACATTGTTGTGATCCGGGAGAACACCGAGGGGGAGTACGCCGGCCTGGAGCACGAGGTCGTCCCGGGTGTTGTCGAGTCTCTCAAGgtac--tccaatttcttctcctctgctttgctcggccgctccagc---tacgtttcttcttgcgcaccag------------------------------

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|110356554|gb|EC919465.1|EC919465
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|351053693|gb|FQ440203.1|FQ440203
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAGCGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|351048104|gb|FQ442074.1|FQ442074
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|161713512|gb|FC063119.1|FC063119
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|110369366|gb|EC933524.1|EC933524
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|161713074|gb|FC062155.1|FC062155
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|161714849|gb|FC063000.1|FC063000
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
EST: gi|161708773|gb|FC060065.1|FC060065
EST:     ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAG                         GTGATGACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT
genomic: ACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctg ... gctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tataaaa