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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttctttgcatcgaaaacttggttcaattttgtctgttattaatgaatttgagatgaaatgattctgcag

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttct--ttgcatcgaaaacttggttcaattttgtctgttattaatgaatttgagatga--aatgattctgcag-------------
 || ||||||  |||  | |||||||| |||||||||||||| ||||||||||| || |||||||| || || ||||| |||||  ||||| |||| |||||  ||  ||  ||||    || |||  |    |   | |   |||||   |    ||    | |     ||  | |    || ||              
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttctttgcatcgaaaacttggttcaattttgtctgttattaatga-atttgagatgaaatgattctgcag------------------------
||| |||||  ||||| | |||||||| || ||||||||||| ||||||||||| || ||||| ||||| || ||||| |||||| ||||| |||| |||||         | |||||| || |   |  || ||||   | ||  ||||| |  |      |  |||      | |  | ||                         
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtc--------ctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagactgctcgctcttccattcttcttatgctatttatgataac

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 7
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttctttgcatcgaaaacttggttcaa----ttttgtctgttattaatgaat--ttgagatgaaatgattctgcag--------------
||| ||||||  |||| | ||||| || || |||||||| || ||||||||||| || ||||| ||||| || ||||| |||||| ||||| |||| ||||| | |||   |  | | || ||||  | | ||  |   |    || | |    |  | |  | |    |   |   ||| ||||   |              
AGAAAGCTTTGAGTACCTTGATGCCCCAGTTGAGAGGATCGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCACAGgtcttttt---ctttgccttccatctgagattttctattagctgttgtatacactgcttaaaactgcccgctcttccatgtttcttatgctatttatgataac

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA14G02380.1 (Glycine max), 5'ss of exon 13
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgt--ttgtttt-----gtcccttctttgcatcgaaaac--ttggttcaattttg----tctgttattaatgaatttgagatgaaatgattctgcag----
 ||||| |||   ||  | ||||||||||| ||||| ||||| || ||||||||||| ||||| |||||||| || || || ||| ||||| | || |||||  | ||| |      |   || ||| |   ||      |  |    |||| |    | |||| | | |   ||     |||||||  | || |     
GGAGAGTTTTGGTTATCTAGATGCACCGGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatggttcttaaatattaattgttttctgtgacttttgtcagcatgatttggaagatttgttttcattattttgatcctgaaatgtatttgtattttg

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA02G46380.1 (Glycine max), 5'ss of exon 13
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgt-----ttgtt---------ttgtccctt----ctttgcatcgaaaacttggttcaattttgtctgttattaatgaatttgagatgaaatgattctgcag
 ||||| |||   ||  | ||||||||||| ||||| ||||| || ||||||||||| ||||| |||||||| || || || ||| ||||| | || |||||     || ||         ||||    |    |||||     |  | ||||   |  ||| |   |||||  |||    || ||| | |  |  |    
GGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatgattcttaaatattaattgttttctgtgactttgtcagcatgatttggaagatattttttcattattt-tgatccagaaatgtatttctattttga

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 13
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgt-----ttgtt-----ttgtcccttctttg---catcgaaaacttggttc--aattttgtctgttattaa--tgaatttgagatgaaatgattctgcag
||| || |||   ||  | |||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| || || || ||| ||||| | || |||||     || ||     ||     || | ||   | | |  | | || ||   ||  ||   ||| ||||   |||    || ||| | |  |  | |  
AGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatgattcttaaatattaattgttttctgtgactttgtcagcatgatttggaagatttgttgtcattattttgatccagaaatgtatttctatttcga

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 14
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgt-----ttgttttgtcccttct---ttg-------catcgaaaacttggttcaattttgtctgttattaatgaatttgagatgaaatgattctgcag--
 |||||||||   ||  | |||||||| || || |||||||| || ||||||||||| ||||| ||||| ||||| || |||||| ||||| | || |||||      | |||||   |||||   |||        |||  || ||    |   |      ||     ||| |||||| |     ||| || |  |   
GGAGAGCTTTGGTTATCTTGATGCACCAGTGGAAAGGATTGCCGGGGCTGATGTTCCCATGCCTTATGCTGCTAATCTCGAGAGAATGGCTGTCCCACAGgtagattcttttttgattcttctagcttgattttattatcataagctcttgttcttccaccttgcatccaataaatttgggtatccatgtttttagatta

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 13
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgt----cccttctttgcatcg---aaaacttggttcaattttgtctg----ttattaatgaatttgagat----gaaatgattctgcag--
 |||||||||   |   | |||||||| ||||| ||||||||||| || ||| |||| ||||| |||||||| || || |||||| |||||||||| ||||| ||  |  |      || |||||  |       || |   ||| |  |||| |     ||  |  |||  | || ||    |   ||    || |   
GGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGAATGGCTCTTCCACAGgtatgcatcctgatattctcctttgtttttcttgtaattacattctacattgtttcagatttgctggtgatctggaaatttatggcctgtccttggaatt

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|164082090|gb|ES148075.1|ES148075
EST:     TTGGCTCTTCCTCAG                         ATAGAGGACATCGTTCGTGCATCAAAGAGAGCTTGTTACAGATCGAAATAA
genomic: TTGGCTCTTCCTCAGgtttgttttg ... gattctgcagATAGAGGACATCGTTCGTGCATCAAAGAGAGCTTGTTACAGATCGAAATAA
EST: gi|125281991|gb|EL296076.1|EL296076
EST:     ATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAG                         ATAGAGGACATCGTTCGTGCATCAAAGAGAG
genomic: ATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttg ... gattctgcagATAGAGGACATCGTTCGTGCATCAAAGAGAG
EST: gi|124737379|gb|EH828781.1|EH828781
EST:     CTAGAGAGATTGGCTCTTCCTCAG                         ATAGAGGACATCGTTCGTGCATCAAAGAGAGCTTGTTACAGATCGAAATAA
genomic: CTAGAGAGATTGGCTCTTCCTCAGgtttgttttg ... gattctgcagATAGAGGACATCGTTCGTGCATCAAAGAGAGCTTGTTACAGATCGAAATAA
EST: gi|124818577|gb|EH903443.1|EH903443
EST:     GTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAG                         ATAGAGGACATCGTTCGTGCATTAAAGAGAGCTTGTTACAGATCGAAA
genomic: GTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttg ... gattctgcagATAGAGGACATCGTTCGTGCATCAAAGAGAGCTTGTTACAGATCGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttctttgcatcgaaaacttggttcaattttgtctgttattaatgaatttgagatgaaatgattctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT