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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatcatggtcctgtctcctcgtactaaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
gtaattgatcatggtcctgtctcctcgtac-taaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC
||||    | || |||||  || | |  || | | |||   |   |  |  | |      |  || |   ||    | ||   |||    |||  |        |||||||| || ||||| || ||||| |||||||||   |||||||| |||||||||||||| |||||    |  ||    |||   | ||| ||||  || |
gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccct--aactggtgttggaaatttt-tgtttt--------tagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 10
gtaattgatcatggtcctgtctcctcgtactaaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataata-ccatgtcctcatctcaat--agGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC
||   | ||  || |  |||    || | ||   ||         ||   | |  ||  |||      |||||   |   ||  ||  | || |   ||  | ||  ||||||| ||||| || || ||||| |||||||||||||||||||||||||| |||||||| ||||||||||  ||   |||||| ||  |||| |  || |
gtgcctaatgttgttattgtgctatcttgctgggtt--------gatttggctc-ctctatccaatttaaatcggcacctatgttaatcttgcctgtattcccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAAAGGCGAATTTAAAGGGC

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 10
----gtaat-tgatcatggtcctgtctcctcgtactaaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataatacc-atgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC
     |||| |  | || || || |||    ||  | | ||  | || | || || || |   |  |        | || | |||||  | |   | |   ||| |    ||||||| ||||| || || ||||| |||||||||||||||||||||||||| |||||||| ||||||||||  ||   |||||| ||  |||| |  || |
gtgcctaatgttgttatagtgctatcttgctgtgtttatttggctcctctatccaatttgaagcggc--------accaatgttaatcttgcttgtattgccattt----agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAATGGCGAATTTAAAGGGC

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
----gtaattgatcatggtcctgt-ctcctcgtactaaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC
     ||||  || || || || | ||    ||  | |  || | |   |||||| || |  | | |         ||| | ||  ||     || |   ||| |    ||||||| ||||| || || ||||| |||||||||||||||||||||||||| |||||||| |||||||||   ||  |||| || |||  ||| | ||| |
gtgcttaatgtattatagttctatacttgctgtgtttatcttgc-ctgtaatgcaatttgactaagcc--------tcaatgttggta----tatatttccattt----agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
gtaattgatcatggtcctgtctcctcgtactaaatttc-caccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC
     || | |  ||  | |       ||||  || |  | |   |||||| || |  | | |         ||| | ||  ||     || |   ||| |    ||||||| ||||| || || ||||| |||||||||||||||||||||||||| |||||||| |||||||||   ||  |||| || ||   ||| | ||| |
----gtgcttaatgtattatagtgctatactttatcttgccctgtaatgcaatttgactaagcc--------tcaatgttggta----tatatttccattt----agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC

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|116438104|gb|EG480696.1|EG480696
EST:     CAATTCAGGAACAGCTGATGCTTGAGAGAGACCCACACGGAAATGTCCAG                         GTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
genomic: CAATTCAGGAACAGCTGATGCTTGAGAGAGACCCACACGGAAATGTCCAGgtaattgatc ... atctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
EST: gi|125019003|gb|EL091272.1|EL091272
EST:     CAATTCAGGAACAGCTGATGCTTGAGAGAGACCCACACGGAAATGTCCAG                         GTTGCTAAGATTGAGACTGA
genomic: CAATTCAGGAACAGCTGATGCTTGAGAGAGACCCACACGGAAATGTCCAGgtaattgatc ... atctcaatagGTTGCTAAGATTGAGACTGA
EST: gi|164037138|gb|ES096619.1|ES096619
EST:     CACGGAAATGTCCAG                         GTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
genomic: CACGGAAATGTCCAGgtaattgatc ... atctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
EST: gi|164057376|gb|ES146762.1|ES146762
EST:     GATGCTTGAGAGAGACCCACACGGAAATGTCCAG                         GTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
genomic: GATGCTTGAGAGAGACCCACACGGAAATGTCCAGgtaattgatc ... atctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
EST: gi|116438054|gb|EG480646.1|EG480646
EST:     CAATTCAGGAACAGCTGATGCTTGAGAGAGACCCACACGGAAATGTCCAG                         GTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA
genomic: CAATTCAGGAACAGCTGATGCTTGAGAGAGACCCACACGGAAATGTCCAGgtaattgatc ... atctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC
                        tattaat  putative branch site (score: 2)
                                        tcctcatctc  putative PPT
             tcacaaatcattatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatcatggtcctgtctcctcgtactaaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG