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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgcatctgtggttcaaatgtaatatttaactttcaagattctgatttagctcataagtttgttctcttctcatatgaccag

Basic information

species Arabidopsis thaliana
transcript AT1G13060.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13060.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 5'ss of exon 6
TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgc--atctgtggttcaaatgtaatatttaactttcaagattctgatttagctcataagtttgttctcttctcatatgaccag--------
|||   ||||  ||| ||||||| |||||| | |||||||||||| |  | || ||||| || |||||||||||||| || ||||||||   || |||||||  |   ||||  | |   ||| || ||||    | |||| |   | | |  |||   |||    ||||   |    | ||  | ||  || |           
TACCGCTATGTGATGCCAGTTGAGGAAGCTGCTGAGTTAGCAAGGCGGGCTATTTACCAAGCTACATTCCGTGATGGGGCAAGTGGTGGTTGTGTTAGCGgtatgctttctgtttaccggtctctgcttca----tgatatctc-ttgtgataatttctattcctgtcatgtttccactttccacacaactgtctgccttaatta

upper sequence: AT1G13060.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA04G37030.1 (Glycine max), 5'ss of exon 7
TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgcatctgtggttcaaatgtaatatttaact-ttcaagattctgatttagctcataagtttgttctcttctcatatga-ccag-------
|||   |||||  |||||||||| |||||| | ||  | ||  |  || |||| || ||||| ||||| |||||||| ||||||||||||||||||||||||   |    |     |  ||     |  |   |||  | || || || | ||     |||||| |  ||   |    |||  |    || |   ||       
TACCGGTATGACCTGTCAGTTGAGGAAGCTGCTGAACTTGCTCGACGAGCAATTTATCATGCAACATTTCGTGATGGGGCCAGTGGTGGAGTTGCTAGCGgtatctttctttctccccactacatctacatgctaacttctatctgtttatgac----atttagttgttatcctctccctcaccagcaataaattagtatttac

upper sequence: AT1G13060.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 7
TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgcatctgtggttcaaatgtaatatttaactttcaagattctgatttagctcataagtttgttctcttctcatatgaccag----------------
|||  ||||||  |||||||||| |||||| | ||  | ||  |  || |||| || || || ||||| |||||||| ||||||||||||||||||||||||    | |||   |   ||      | | || ||     ||||||  |    |||| ||||   |||    ||| | || |||| | |||||||                
TACCGATATGACCTGTCAGTTGAGGAAGCTGCTGAACTTGCTCGACGAGCAATTTATCACGCAACATTTCGTGATGGGGCCAGTGGTGGAGTTGCTAGCGgt----actctttctttctcccccact-atatctacatactaacttcta----tctg-tttatgacattttgttgctatcctctc-tctgaccagcaataaattagtattt

upper sequence: AT1G13060.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 5'ss of exon 7
TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgcatctgtggttcaaatgtaatatttaactttcaagattctgatttagctcataa-gtttgttctcttctcatatgaccag------
|||   ||||||||||| ||||| |||||| | || || || ||  |||| || || ||||||||||||||||||||||| |||||||||||||| ||||||   || |||   |   ||| |   ||   | |       |  |    | || |  || ||  |  |   ||||    | |   ||| |            
TACCGTTATGATATGTCTGTTGAGGAAGCTGCTGAATTGGCTAGACGATCTATTTATCATGCGACATTCCGTGATGGAGCTAGTGGTGGAGTTGCAAGCGgtacttactctctctctctctctctctctc-tctctctcccatgtggatacatacaaatgtatgtagttgtgtttacggtttaaacatgtattttttgttag

upper sequence: AT1G13060.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S39_347V6.1 (Physcomitrella patens), 5'ss of exon 6
TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgcatctgtggttcaaatgtaatatttaactttcaagattctgatttagctcataagtttgt-tctcttctcatatgaccag------------------------
|  || |  ||||||||  | || |||||    ||| | ||  |  | || || ||||||||||| |||||||||||||| |||||||| || | ||| ||| || |||  |||||| | |    |   ||   |   || |  |  |      ||  | |  ||    |||  || ||| || |||      |                          
TTTAACTGGGATATGTCTATCGACGAAGCAGTAGAGCTTGCTCGTCGTTCTATTTACCATGCGACTTTCCGTGATGGAGCTAGTGGTGGTGTAGTTAGTGgtaagcaat--gaatgcttttcctttctcaacagatcgttcagatgccttttgccttgtctttctgtgcagtcagtctctgttgtcaagaattctctcttaagtctttgttggtctgcag

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|125030917|gb|EL103186.1|EL103186
EST:     TGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCG                         TGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGT
genomic: TGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatc ... atatgaccagTGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGT
EST: gi|125165304|gb|EL191648.1|EL191648
EST:     GGAGTTGCTAGCG                         NGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
genomic: GGAGTTGCTAGCGgttagtaatc ... atatgaccagTGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
EST: gi|164151657|gb|ES039442.1|ES039442
EST:     CATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCG                         TGTACCACGTTGGTCCCGAAGGATGGACCGAAACTATCAGGAGATGATGTT
genomic: CATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatc ... atatgaccagTGTACCACGTTGGTCCCGAAGGATGGAC-GAAACTATCAGGAGATGATGTT
EST: gi|125311197|gb|EL325282.1|EL325282
EST:     GATGGAGCCAGTGGTGGAGTTGCTAGCG                         TGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
genomic: GATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatc ... atatgaccagTGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
EST: gi|86079424|gb|DR375181.1|DR375181
EST:     AATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAG-S                         TGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
genomic: AATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatc ... atatgaccagTGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
EST: gi|116463327|gb|EG505919.1|EG505919
EST:     AATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCG                         TGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG
genomic: AATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatc ... atatgaccagTGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGCGgttagtaatctgaatgcatctgtggttcaaatgtaatatttaactttcaagattctgatttagctcataagtttgttctcttctcatatgaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG