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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttcattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag

Basic information

species Arabidopsis thaliana
transcript AT1G08200.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttcattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag
||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||||||  |||||||||| |||||||||||||||||  |  ||||||| ||  ||| |       | ||||| ||||           ||||||||||   | |||   | | |   ||||| | ||||  |     |  |  ||
TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgc----gtttatctctggc-------tccttgtttttatgc-actaatccaat-gaggctgaact-cttgttgtcaattgcaaaag

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G19550.2 (Glycine max), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttca---ttcattgcttatccctggtgatatatcgtttgtttttatattatta-aagaagttgcatctgaattgcttgcggaattctttaccag
|||||| ||| | ||||| |||||||||||||| |||||  | || |||||||||||||| ||||| ||||||||||| ||||||||| | |||||||| ||  |||  |   | |  |  ||||   |||   | | |   || |   || |   | |   ||  ||   ||    |   ||   |   |  | | | |
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctg

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttca---ttcattgcttatccctggtg--atatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag----------------------------
|||||| ||| | ||||| |||||||||||||| |||||  | || |||||||||||||| ||||| ||||||||||| ||||||||| | |||||||| ||  |||  |   | |  |  ||||   |||     | | |  |||   |  | |||  |     | ||     ||      |   |   || |   |  |                            
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacag

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttcattcattgcttatccctggtgatat-atcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaat----tctttaccag--------------------------------
||||||  || | ||||| |||||||||||||| |||||  | || |||||||||||  | ||||| ||||||||||| ||||||||| |  ||||||| ||  |||  | |    |  ||||  |  |  |   |  ||||||||||  | ||  | | | ||  ||| ||| ||  ||    | |    |  ||    |                                
TCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGATTgtacgttctaat----gtctatctttatttttgggactgtttgttttttaaataccatacaggtc-catgtgatttttttttcaagtcaaattattgttggctggtccactgagtgttatgacctgttaacag

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G30490.1 (Glycine max), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttc---attcattgcttatccctggtgatatatcgtttgtttttatattattaaag---aagttgcatctgaattgcttgcggaattctttaccag------------------------
||| || ||  | ||||| ||||||||||||||||||||  |||| ||||| || ||  | || || || |||||||| ||||||||| | |||||||| ||  ||| |   || || |  || |         |||||  |||   ||   ||| |  ||    |  ||  | ||    | ||||  | ||  || | |                          
TCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGATTgtaggttcccatatccaatctttttatgcaactttatatattttaagttctgattgtagaatttcatctttaaactattattcttgttggatggttcaactaaatgtgaacgataatttttaacag

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagttt-cattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag
 ||||| || || ||||| ||||||||||||||||||||  |||| |||||||||||  | || || || |||||||| ||||| ||| | |||||||| |||||||  |  || || |||        ||||    | |||  ||| |  |    ||| ||    ||      |   |      ||  |||  |||
CCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgtgagttgaccatcctttctttcattatatgattccacatttagttt-acttggaaaaaaaaaaaacaggatgctgaatattatgatcttttctcag

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagttt-cattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag
 ||||| || |  ||||| ||||||||||||||||||||  |||| |||||||||||  | ||||| || |||||||| ||||| ||| | |||||||| || |||   |  || || |||        ||||    | |||   || |  |    ||| ||   |   ||||||    ||    ||  |||  |||
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacatttagctt-acttggaaaaaaaaaaggttgctgaatactatg----atattttctcag

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|116471821|gb|EG514413.1|EG514413
EST:     GAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATC                         GAAAATCCAGAGAGAGCCAATGGGCATATCTTCAATGTAGGCAACCCAAAC
genomic: GAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttca ... tctttaccagGAAAATCCAGAGAGAGCCAATGGGCATATCTTCAATGTAGGCAACCCAAAC
EST: gi|124712407|gb|EH803809.1|EH803809
EST:     ATCGAAGCTGTCCTTTTGATGATC                         GAAAATCCAGAGAGAGCCAATGGGCATATCTTCAATGTAGGCAACCCAAAC
genomic: ATCGAAGCTGTCCTTTTGATGATCgtgagtttca ... tctttaccagGAAAATCCAGAGAGAGCCAATGGGCATATCTTCAATGTAGGCAACCCAAAC
EST: gi|125255338|gb|EL269423.1|EL269423
EST:     TCGAAGCTGTCCTTTTGATGATC                         GAAAATCCAGAGAGAGCCAATGGGCATATCTTCAATGTAGGCAACCCAAAC
genomic: TCGAAGCTGTCCTTTTGATGATCgtgagtttca ... tctttaccagGAAAATCCAGAGAGAGCCAATGGGCATATCTTCAATGTAGGCAACCCAAAC
EST: gi|164104724|gb|ES087553.1|ES087553
EST:     GAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATC                         GAAAATCCAGAGAGAGCCAATGGGCATA
genomic: GAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttca ... tctttaccagGAAAATCCAGAGAGAGCCAATGGGCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttcattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG