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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacatagctatgttaattaatcagctgaggtaaatacaaatgtgtgtttggcggttgaaaattgtgttgatcgttttgtag

Basic information

species Arabidopsis thaliana
transcript AT1G75380.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA14G07830.1 (Glycine max), 5'ss of exon 7
GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgta--------ttacatagctatgttaat---taatcagctgaggtaaatacaaatgtgtgtttggc--ggttgaaaattgtgttgatcgttttgtag--
|| || |||| | | || | ||| |||||||||||| | ||||||||||| |||||||| || || ||||||||||||        | |  ||| ||| | |||   | ||   |||      ||   | | | |  ||||   | ||   | ||||     |  |    | |  
GTTGGAAATGACGCAGAATATGTGAGCTTTGATCTTCGACCTTCAGATGCTATCAATATTGCAGTAAGATGCAAGgtaatatttgttaatttaggtatttgaatacatcattgactgcatcgtattgcattctcttattggtttgtttagtagttgttcactttttcccctggtt

upper sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA17G37160.1 (Glycine max), 5'ss of exon 4
GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacat--------agctatgttaat---taatcagctgaggtaaatacaaatgtgtgtttggc--ggttgaaaattgtgttgatcgttttgtag--
|| || ||||   | || | ||| |||||||||||| | ||||||||||| ||||| || || || |||||||||||| ||  |        || ||| | |||   | ||  ||||    | ||   | | | |  |||    | ||   | ||||     |  |    | |  
GTTGGAAATGAGGCAGAATATGTGAGCTTTGATCTTCGACCTTCAGATGCTATCAACATTGCAGTAAGATGCAAGgtaatatttgttaattaaggtatttgaatacatcattggctgcatcatattgcattctcttattgctttgtttagtagttgttcgctttttcccctggtt

upper sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacatagctatgttaattaatcagctgaggtaaatacaaatgtgtgtttggcggttgaaaattgtgttgat--cgttttgtag---------------
||||||||||     ||| | ||||| ||||| ||| | ||||||||||| || || || |||||||||||||||||| | | |   | ||    | | |    |||  | | ||||    | | |||||     | |  || ||  |||  |  | ||||                
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtact-cttcattgtgggtgtgagttgtgtgacttta-tacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt

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|125165719|gb|EL191857.1|EL191857
EST:     TTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAA
genomic: TTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAA
EST: gi|125014379|gb|EL086648.1|EL086648
EST:     GCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACA
genomic: GCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACA
EST: gi|124765239|gb|EH855369.1|EH855369
EST:     TGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAATGAGAGTC
genomic: TGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAATGAGAGTC
EST: gi|124841699|gb|EH926136.1|EH926136
EST:     ATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAAT
genomic: ATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAAT
EST: gi|124933159|gb|EL010346.1|EL010346
EST:     CTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTG
genomic: CTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTG
EST: gi|124950468|gb|EL025930.1|EL025930
EST:     TGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGGATGAGAGTC
genomic: TGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAATGAGAGTC
EST: gi|125267128|gb|EL281213.1|EL281213
EST:     CTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAATGAG
genomic: CTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAATGAG
EST: gi|47829045|gb|CK118729.1|CK118729
EST:     GCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGNTAGATGCANG                         ATACCTATCCAAGTGA
genomic: GCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGA
EST: gi|124919417|gb|EH993180.1|EH993180
EST:     AGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTGCCTTGCATATAGTGATGGAATGAGAGTC
genomic: AGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAATGAGAGTC
EST: gi|124962397|gb|EL036823.1|EL036823
EST:     ATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAA
genomic: ATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATAGTGATGGAA
EST: gi|124769256|gb|EH859386.1|EH859386
EST:     CTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCAAGTGAACAAGTACCTTGCATATA
genomic: CTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCAAGTGAACAAGTACCTTGCATATA
EST: gi|125077190|gb|EL140068.1|EL140068
EST:     GCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG                         ATACCTATCCA
genomic: GCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacata ... cgttttgtagATACCTATCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacatagctatgttaattaatcagctgaggtaaatacaaatgtgtgtttggcggttgaaaattgtgttgatcgttttgtag

- - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT