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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttactagttactagtactactagtaatttctatgcttccaatcttacttcttgtagtactatcatattatatcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------gtaatttactagttactagtac-----tactagtaatttctatgcttcca---atcttacttcttgtagtact--atcatattatatcagtgaggaattgaccttattatgc-attccactcga---acagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
                                                    | || | | |   | |||||       | ||  |  | | |||| ||  |      | | || |   || | |  | |  ||| | | |  |  |||   |  || | |  | |  | ||||     |||||| |||||||| ||||||||  | || ||||| ||||||||||| || ||||| || ||||||||||| ||||||||||| ||||| |||||||| || |
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaatt--ctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgt-taaaggtagaacatattttctaacaccaggctactctgtttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
gtaatttactagttactagtactactagtaatttctatgcttccaatct-tacttcttgtagtactatcatattatatcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
        |||    || |  || |     ||  | |||   | ||| | | || | |||   |  ||||   |||| ||  |   | ||    |||  |  | |    |||  |||||| |||||||| ||||||||  | |||||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||| |||||||| ||||| || |
--------ctatcctctggccctgc-----ataacgatgagccaaatatattctacatgtgacataatcagtgtatagcacagcatattt----ttaacac-cttgatcctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 8
gtaatttactagttactagtactactagtaatttctatgcttccaatct-tacttcttgtagtactatcatattatatcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
               |   | | ||   ||||    |  |   || | | ||  | |   |  | ||   ||| ||| |||       || ||      || |  ||   |  | ||||| || || || ||||||||  | |||||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||| |||||||| |||||||| |
---------------cccctgc-acacataatcatgagccaatcattttctaaatttgacataattagtgtataata-cagcatatttttaacacctcaattctctctgtttta-cagGCTAACGACCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCGGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTTATCT

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 8
-------gtaatttactagttactagtactactagtaatttctatgctt-ccaatcttacttcttgtagt---actatcatattatatcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
        ||||    || |  ||  | ||| |  |  | | || | |   |  ||| | ||| | |||    |      | || | ||  | |  | |||   | || |||     |  | | ||||||||||||||| ||||| ||  | |||||||||||||||||||| || ||||| || ||||||||||||||||| ||||| |||||||| || |||||||
gtatcaattaataatttaatctcttatcctaattatgttgtttaggatgatctctctcatttcatttaggtggaagggtgttttttttcttttaatatttg---taatgatgtggctcttttgcacagGCCAATGATCCCACCATAGAACGCATTATCACTCCTCGAATTGCTCTCACAACTGCAGAATATTTGGCTTATGAGTGTGGGAAGCATGTTCTAGTTATAT

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaatttactagttactagtactactagtaatttctatgcttccaatcttacttcttgtagtactatcatattatatca---gtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
                    |  | |  |   ||| || |   |  ||||  | || | |  | |    |  ||  ||     |   ||||| |  ||   ||   |      |   ||||| ||||||||||| |||||  | ||||||||||||||||| ||||| || || |||||||| |  |||||||||||||| |||||||| || || ||  
------------------aaatcaatgtt--cttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatttactagttactagtactactagtaatttctatgcttccaatcttacttcttgtagtactatcatattat-atcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
                   |  | | |    | |||  | |  |  | | |  | | |||   |  |  |   |  | || |  |   || |  ||   ||  || |   |    ||||| ||||||||||| |||||| | || ||||||||||||||||| || || || ||||||||||  |||||||| ||||| ||||||||| | || ||| 
-----------------catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttg-cagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------gtaatttactagt-tactagtactactagtaatttctatgcttc-caatctta--cttcttgtagtactatcatattatatcagtgaggaatt----gaccttattatgcattccactcgaac----agGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
                                                                        | |||  |    || | | |          |||  |  |||| |||  | |   ||| |  ||| ||  | | || |  | |     | ||     |  ||||| |    ||  || |  |    |||| ||||||||||| |||||| | |||||||| ||||||||||| || ||||| ||||| || |  |||||||| ||||||||||| || || || ||  
gtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcagGCTAATGATCCAACAATTGAGCGTATTATCACACCTCGAATTGCACTTACAACTGCTGAGTACTACGCTTATGAGTGTGGAAAGCACGTTCTGGTCATCC

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|116483049|gb|EG525641.1|EG525641
EST:     ATTTTGAAGAAAATGGATCGATGGAAAGGGTTACCCTTTTCCTGAACTTG                         GCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAAT
genomic: ATTTTGAAGAAAATGGATCGATGGAAAGGGTTACCCTTTTCCTGAACTTGgtaatttact ... actcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAAT
EST: gi|124946747|gb|EL022638.1|EL022638
EST:     TTTCCTGAACTTG                         GCCAATGATCCAACCATTTGAGAGAATTATCACTCCTCGAATTGCCCTAAC
genomic: TTTCCTGAACTTGgtaatttact ... actcgaacagGCCAATGATCCAACCA-TTGAGAGAATTATCACTCCTCGAATTGCCCTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatcatattatatcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT
                       aattgac  putative branch site (score: 3)
                                         ttccactc  putative PPT
      atattatatca  TA-rich tract