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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgttccctgtgccttgtttcgtttcagttgtggtgtgcttacttgtgctctcctgtatttgatctttag

Basic information

species Arabidopsis thaliana
transcript AT1G10290.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgttccctgtgcct-tgtttcgtttcagttgtggtgtgcttacttgtgctctcctgtatttg---atctttag--------------
||  | || ||||| ||||| ||||||||||||||||| ||||| ||||| ||||||||    ||||||||  ||   | ||| |||  |||   | ||  | |  | || | | |  | ||| ||| | |||  ||  ||      | |  |||              
GCAATCGTACTTTGCCAAGTGGAGAAAGCAAAGGAAGATATGCTAAATCAGCTCTACAGCAAAATAAGgtttgatgcgtattctttctttgtatttgtgcattgcataaggtttcgctt-ctttctttttctccactaaatggacatacccctagatggaactgcattg

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgttccctgtg-ccttgtttcgtttcagttgtggtgtgcttacttgtgctctcctgtatttgat-ctttag---------------
||| |||| ||||||||||| ||||||||||||||||||||||| || || || ||||| || |||||||| |   ||| | | ||    ||  | |||||      || | |   |           |||  |||    |||||  ||| |                
GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttctgtacattaatagtttctttgttctcaaacactagacattcagaacaagatgcaatccaacttttgaaacttcaactgtcagtttctaag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GRMZM5G811223_T01 (Zea mays), 5'ss of exon 8
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgtt------ccctgtgcctt-----gttt--cgtttcagttgtggtgtgcttacttgtgctctcctgtat-ttgatctttag---
||| |||| || || ||||| ||||||||||||||||||||||| || || || ||||| || |||||||| | | ||| | | ||      |||| ||   |       ||  | ||  ||    | || | | |||| ||        | | |   | | ||    
GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttctgtacattaatgctccctctgttctcaaacacttgacattctagacaagttgcggtcacttttgaaacttcatctgtcagtttataatat

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgttccct--------------gtgccttgtttcgtttcagttgtggtgtgct-tacttgtgctct-cctgtatttgatctttag-
|| ||||||||||| |||||||||||||| || |||||||||||||| || || ||||||||  | |||||     |||   ||| |  |              |||  ||| ||| |    | | |  |||  | ||||     ||  ||| ||||   || ||   
GCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTGAACCAGCTATACAGTTCCGTCAGgttagtgttctcgccgtactgtctgatgatcattgagtgtgttgcttcttaatggatattatgtaatgtactgccattcaacctatattcactcctttca

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgtt--caatatcttttcgttccctg-tgccttgtttcgtttcagt-tgtggtgtgcttacttgtgctctcctgtat-ttgatctttag------------
|| ||||||||||| |||||||||||||| || ||||||||||| || || || |||||||| || |||||     | ||| |||   || |  || ||  |     || ||| ||| || |  | ||   |  | |    | |  ||   || |             
GCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTCAACCAGCTATACAGTTCCATCAGgttggtgctgtctcttctcgccgtactgtctgatgatcattgagtgtgttgtttcttaacggatattatgtaatgtactggcattcaacctatattcact

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA09G00430.2 (Glycine max), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttca-atatcttttcgttccctgtgccttgtttcgtttcagttgtggtgtgcttacttgtgctctcctgtatttgatctttag-------------------
|| ||||| ||||||||||| || || || ||||||||||||||||||||| | || || ||| | ||||||| |||| | ||  | || | |    |  | |  ||   ||   |  | ||| ||||   |   | || ||   |||| |                    
GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAGgttcagatatttgtttttgccttttattcttatcctcttgcatta--gatttcttccttgcatttgtcagt-ttcattcttgaagattttgaaggaacataaa

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA12G37100.1 (Glycine max), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttca-atatcttttcgttccctgtgccttgtttcgtttcagttgtggtgtgcttacttgtgctc---tcctgtatttgat--ctttag-------------
|| ||||| ||||||||||| || || || ||||||||||||||||||||| | || || ||| | ||||||| | || | ||  | || | |    |  |||  ||   ||    |   ||| ||||   |    ||   |  ||||    ||||              
GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAGgttcagaaatttgtttatgccttttattcttattctcttgcattaaattt--cttccttgcatttcagtctcattcttgaagattttaaaggaacataaaga

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 20
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttca-atatcttttcgttc----------cctgtgccttgtttcgt--ttcagttgtggtgtgcttacttgtgctctcctgtatttgatctttag------
|| ||||||||||| ||||| |||||||| |||||||||||||| |||||  | ||||| || || ||||  | | || ||  | |            ||  | |      || |  || | || |  | ||  || | ||     |  | |||||||| |         
GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagatattcccatataaataaacaacccatacacaaactcatcctttactttttatttgtataat-gtaaaggcg-gaatttgatcctagtcagtac

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 5'ss of exon 19
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgttccctgtgccttgtttcgtttcagttgtggtgtgcttacttgtgctctcct--gtatttgatctt-tag--------------------------------
|| ||||| |||||||||||||||| ||||||||| | |||||| || ||||| || || ||||| |||| |||  |   |   ||      ||  |||||   ||  |||  | ||||||   ||||  ||| ||  |   | | | ||  ||                                
GCAGTTGTCCTTTGTCAAGTAGAGAGAGCAAAGGATGCCATGCTTAACCAACTTTATAGCTCTATCAGgtacaaattagatgaatttggaaagcagtgtttaactt--gtttcgatgtgctggattgttatcttctaagcgctaggtattgcagacagtttgtattcattagtatttgtgtgatag

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|116420913|gb|EG463505.1|EG463505
EST:     GTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAG                         TGCAATAGGCAATGAAAGGATTGAGTCATTGATACAAGAGGGTCAGAATGT
genomic: GTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatc ... tgatctttagTGCAATAGGCAATGAAAGGATTGAGTCATTGATACAAGAGGATCAGAATGT
EST: gi|124781164|gb|EH871107.1|EH871107
EST:     GTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAG                         TGCAATAGGCAATGAAAGGATTGAGTCATTGATAC
genomic: GTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatc ... tgatctttagTGCAATAGGCAATGAAAGGATTGAGTCATTGATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAGgttcaatatcttttcgttccctgtgccttgtttcgtttcagttgtggtgtgcttacttgtgctctcctgtatttgatctttag

- - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - -  ATGCTG