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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaaatccgatctcttctttcttctcttctatctgaatttatctttattagtggatgatgaatgtaattgcgtggtaattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G26550.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G26550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 5'ss of exon 3
GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtcca-aatccgatctcttctttcttctcttctatctg-aatttatctttattagtggatgatgaatgtaat-tgcgtggtaattgcag--------
||||||||||||||||||| || ||||| ||||| || || || || ||||| || ||||  |||||||| ||||  || || ||||| || || |||||||||||  | |||   ||  || |  | ||  || | ||||    | |||    | | |    |   |  | | |  || ||| | ||    |        
GAGATCTTGGATGGTTCCCGCGTGGAAAAATGGCTGGCCCTTTTCAGGATGTTGCATTTAGCACACCTGTGGGAGCTACTAGCGCACCATTTAAGTCAACgtatgtgtataattgtattactaccctttttcctccaatcttcggtctattaacaat-gcaagtagcgcctatgacatgagtgctgatctgtgcgataccg

upper sequence: AT1G26550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G33180.2 (Glycine max), 5'ss of exon 4
GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtc-----caaatccgatctcttctttctt------ctcttctatctgaatttatctttattagtggatga-tgaatgtaattgcgtgg-taat--tgcag
|||| ||||||||||| || |||||||||||||| || ||||| || ||||| ||||| || |||||||||||||  || ||||| || ||||||||||||||| ||     ||      |  | |  |||| |      | | | |  |     |  |||  |||   | |    ||    |  |||| ||| | ||  |||||
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGATGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCAACgtatttctcttgcactcttaacttttattttcctgattagcacctgtgccccttctcttctcaatttaggcacacctgctaatgtttgcttggatgatgatgcag

upper sequence: AT1G26550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G21080.1 (Glycine max), 5'ss of exon 4
GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtcc-----aaatccgatctcttctttctt------ctcttctatctgaatttatctttatt--agtgga--tgatga-atgtaattgcgtggtaat--tgcag
|||| ||||||||||| || |||||||||||||| || ||||| || || || ||||| || |||||||||||||  || ||||| || |||||||| |||||| ||      |      |  | |  |||| |      | | | |  |     |  |||| |||   |  ||  || | |  | |  |||  || | ||  |||||
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctcttgtactcttaacttttattttcctgattagcacctgtgccccttctcttcttcatttaggcagacctgctaatgtttgtttggatgatgatgatgcag

upper sequence: AT1G26550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 5'ss of exon 4
GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaaatccgatctcttctttcttctcttctatctgaatttatctt-tattagtggatgatgaatgtaattgcgtggtaattgcag---------------------------------
| || ||||||||||| || || || |||||||| |||||||| || ||||| ||||| |  |||  | |||||| |||||||||||| ||||||||||||||||     || | |  |    |   || | | ||   ||| || ||  | |||   | |||  | | |   | | || ||||  | ||                                  
GTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCTTCAGCACAGTTATTGGAGCCACCAGTGCACCATTCAAATCAACgtatg----gattcaaatttgggtggtttttatgctcgttgagttaattctgtatctctagattcttagtactact-cg-ggtagcttcaactagctaaccttattttgcttttgatcatgcag

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|86025350|gb|DR321103.1|DR321103
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTG
EST: gi|86025343|gb|DR321096.1|DR321096
EST:     TCGCCTTTAATACACCTGTTGGAGTCACCCAGTGCACCCTTCADATCAAC                         GCACGGATACCACATTATT
genomic: TCGCCTTTAATACACCTGTTGGAGTCACC-AGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATT
EST: gi|86025368|gb|DR321121.1|DR321121
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGG
EST: gi|86025338|gb|DR321091.1|DR321091
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTTATCAGAGGGAAGGAAGAACTGACAGATAC
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTT-ATCAGAGGGAAGGAAGAACTGACAGATAC
EST: gi|86025345|gb|DR321098.1|DR321098
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025358|gb|DR321111.1|DR321111
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025346|gb|DR321099.1|DR321099
EST:     TCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTTCAA-TCAAC                         GCACGGATACCACATTATTTTA
genomic: TCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTT-CAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTA
EST: gi|86025370|gb|DR321123.1|DR321123
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025355|gb|DR321108.1|DR321108
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGA
EST: gi|86025333|gb|DR321086.1|DR321086
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCCACGGATACCACATTATTTTATCAGAGG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGC-ACGGATACCACATTATTTTATCAGAGG
EST: gi|86025347|gb|DR321100.1|DR321100
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAG
EST: gi|86025339|gb|DR321092.1|DR321092
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025342|gb|DR321095.1|DR321095
EST:     CGCCTTTAATACAACCTGTTGGAGTCACCAGTTGCACCCTTCAAATCAAC                         GCACGGATACCACATTAT
genomic: CGCCTTTAATACA-CCTGTTGGAGTCACCAGT-GCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTAT
EST: gi|164046161|gb|ES167116.1|ES167116
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTA
EST: gi|86025344|gb|DR321097.1|DR321097
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGG
EST: gi|86025369|gb|DR321122.1|DR321122
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGAATAC
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGA-TAC
EST: gi|86025361|gb|DR321114.1|DR321114
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAG
EST: gi|86025341|gb|DR321094.1|DR321094
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025335|gb|DR321088.1|DR321088
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAG
EST: gi|86025362|gb|DR321115.1|DR321115
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTT
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTT
EST: gi|86025372|gb|DR321125.1|DR321125
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATC
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATC
EST: gi|86025349|gb|DR321102.1|DR321102
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025353|gb|DR321106.1|DR321106
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGAT
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGAT
EST: gi|86025331|gb|DR321084.1|DR321084
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGA-CTGACAGA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGA
EST: gi|86025348|gb|DR321101.1|DR321101
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGG
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGG
EST: gi|86025357|gb|DR321110.1|DR321110
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATACA
EST: gi|86025340|gb|DR321093.1|DR321093
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACCTGACAGATAC
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAAC-TGACAGATAC
EST: gi|86025332|gb|DR321085.1|DR321085
EST:     GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAAC                         GCACGGATACCACATTATTTTATCAGA
genomic: GTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGA
EST: gi|164126310|gb|EL999484.1|EL999484
EST:     GTGCACCCTTCAAATTCAAC                         GCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATAC
genomic: GTGCACCCTTCAAA-TCAACgtatgtccaa ... gtaattgcagGCACGGATACCACATTATTTTATCAGAGGGAAGGAAGAACTGACAGATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtccaaatccgatctcttctttcttctcttctatctgaatttatctttattagtggatgatgaatgtaattgcgtggtaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG