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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcag

Basic information

species Arabidopsis thaliana
transcript AT1G13320.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 10
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtt-tgtgtagaa-atcttaagcatatagtatgttttcaatt--caaatc---gagcattttagctattggttattggagtatatttacttgttcag---
||   ||||||| | || ||||||||||||||  ||||||| || ||||| ||||||||||| |||||||| |||||||||||| | ||||||||| | | || || || | || | ||     | ||| || ||   |||||    ||||   |  || ||   || || ||      |    ||   |   
GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttataaaatatttgaaccctagtcagtatttgcatttgtgaaatccttaagcaagctgacttttttgtaatgtagctctactggaagtctggaac

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtt-tgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatt-tacttgttcag
||   ||||||| | || ||||| || |||||  ||||||| ||||| |||||||| ||||| || |||||||||||||||||| ||||||||||| | | |  |     | |  |  | |||| |  |  |         |  ||  |  ||  |  ||  || |   | || |  ||   |||
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtcaataccttgtatttcctacaactgtgcataatataatc-cttctatttcctgcaacctgttctgttttcccag

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G164352_T03 (Zea mays), 5'ss of exon 10
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcag--------------
||    |||||| | || ||||| || |||||  ||||||| ||||| |||||||||||||| || |||||||||||||||||| | |||||||||  | || | |   |    |||   ||| ||| | |    ||  | ||  |  |     |  |  |||  |   ||||| || |  |               
GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAGgtt-atttatatactatctcaataccttatatttcctac---aactgtgctgtgcataatataatccttgatgctaatttatttatcaacagtagctacaacat

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcat-----atagtatgttt--tcaattcaaatcga--gcattttagctat-tggttattggagtatatttacttgttcag----------------------------------------------------------------------------
||||| ||||| |||||||| ||||| |||||  |||| || ||||||||||| ||||||||||| ||||| |||||||| ||| |||||||||||  | ||   |  | |   ||     |    ||| |    |||   |  || |    | ||   || | ||| | || | | || | |     |  |                                                                             
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcag------------
||||| || |||||||| || ||||| |||||| ||||||| || |||||||| ||||||||||| ||||| ||||| || ||| |||| ||||||  |||      |||||| || || ||| |    | |  | |    || | |  |    || || |    |||| |||   | |                
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttgg-cttaagaat-tattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgta-------gaaatcttaagcatatagtatgttttcaattcaaatcga--gcattttagctat-tggttattggagtatatttacttg---ttcag---------------------------------------------------------------------------------
||||| ||||| || ||||| ||||| |||||  |||| || ||||||||||| ||||| ||||| ||||| |||||||| ||| |||||||||||  | ||        |  | |||   |   | |       |||   |  || |    | ||   || | | | | || | | || | || | |   || |                                                                                  
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 9
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcatatagta-tgttttcaattca-----aatcgagcattttagctattggttattggagtatatttacttgttcag----
||| |||| || ||||| |||||||| |||||  | ||||| ||||| ||||| ||||||||||| ||||||||||||||  || |||| ||||||||| |||   |  | |  ||  | |  | ||      |        || | | || | || |     || |     ||| |    ||| |  |    
GTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAGgtttgtctagtggttgtgacaattaattgctattagtggcttgtaaaggatagtggatatgagtttcaaattctcatcttatttcattttggtttgtctc

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtg---tagaaatcttaagcatatagtatgttttcaat-----tcaaatcgagcattttagc-tattggttattggagtatatttacttgttcag--------------------------------------------------------------------
||  |||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||||||||| |||||| ||||||| ||  |||| |||||    |   || ||   |  ||     | ||| ||   ||      |  ||||| |   |||  | ||  |   |     || ||| |    | || |                                                                    
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag

upper sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgt--ttgtgtagaaatcttaagcatatagtatgtttt--caattcaaatcgagcattttagctatt-----ggttattggagtata---tttacttgttcag-------------------------------------------------------------------------------------------------
||  |||| ||||| || |||||||| ||||| || ||||||||||| |||||||| ||| | || |||||| |||| || ||  |||| |||||  |||      ||  ||  | ||   || |   |    |||    || ||   | | ||||  |      ||   |  | || |   |||  | ||| |                                                                                                  
GTGTACTCTATCCGAGAGGCTGCTGCGAACAACCTTAAGCGTCTTGCCGAAGAGTTCGGTTCCGAGTGGGCATTGCAACACATCATTCCACAGgtacttgcccgacaagtttgtg-atgaggtctaactcggtaatgagtatggaagttatgagcttctctcacagtcgatacattacagcctttgttcgttaaacacacgagctatggttgagagacctgtgtatttgtgataatttttatactactgataggctgagatttttttctgaccatgttgtgaggacttgcag

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|116425639|gb|EG468231.1|EG468231
EST:     TTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG                         GTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTT
genomic: TTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtag ... acttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcag

- - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA