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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtctcttagcctagaggattactcctgattatatgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT

Basic information

species Arabidopsis thaliana
transcript AT5G50320.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 2
------------gttagagtttgatatttctagtaacctgtg-agtattattttcgttctttttaccagtctcttagcctag---aggattactcctgattatatgaatga--cagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
              | |||  || | | |||  |    || | | |   |||  | ||||  ||||   |   | |  |||    | | |||       ||  ||  || |  ||||| || ||||| |||||||| || |||||||||||| | || ||||| ||||||||||  |||||  | |||||||||||||| ||||| ||||||||||
gtttgcccttacccttgagagtgttgtgtct--tggtttgagtaattcgattcactttctagttacatttgattaatgctatcataagtttaaaataatttgaatacattatgcagGTCGAATTCATATTGATGGGTGGAACTTTCATGTCATTACCAGCTGATTATCGGGATTATTTCATTAGAAATCTTCATGATGCCTTATCGGGACACACTT

upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G359735_T03 (Zea mays), 3'ss of exon 2
----gttag-agtttgatatttctagtaacctgtgagtatt-attttcgttctttttac-cagtct-cttagcctagaggattactc----ctgattatatgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
    || || |||   | |   |   |  |  |    |||| | | |  |  |    ||   || |  | |   | ||  |  | |      |||| || |   |  ||||| || ||||| |||||||| || |||||||||||  | || ||||| ||||| ||||  |||||  | |||||||||||||||||||| || |||||||
gtttgtcagtagtccaagacagcacttggctcgattttattgactcttatgttcacgacatggtgtattcaattttgaccagcagttgaagatgataatgtactttgcagGTCGAATTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGAATATCGTGATTATTTCATCAGAAATCTTCATGATGCTTTATCGGGTCACACTT

upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
-----gttagagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtct---cttagcctagaggattactcc----tgattata---tgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
       | ||||   | |   |    | |       ||||  ||    | ||     ||  ||    | |   | ||  |  | |      ||||||||   |  ||  ||||| |||||||| |||||||| || |||||||||||  | || ||||| ||||| ||||  || ||  | ||||||||||||||||| || || |||||||
gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT

upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 2
gttagagtttgatatt--tctagtaacctgtgagtatt---attttcgttcttt--ttaccagtctcttagcctagaggattactcctgattata----tgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
      ||||||   |  | |  || |   ||| ||||   ||    || | |    |   |||   ||  |   | | | | ||  | | |||     |   |  ||||||||||| || || ||||||||||| ||||||||||| || ||||| || || |||| ||| ||| | ||||||||||||||||| || |||||||| |
------gtttgaagctcattttatatctcttgaatattccaatccaagtacatgaaatgagagtagatttactgtgtgaagtccttgtaactatggttgttgttttcagGTTGAGTTTATCTTAATGGGAGGTACCTTCATGTCACTTCCGGCTGATTACCGTGATTACTTTATAAGAAATCTTCATGATGCTTTGTCTGGACACACAT

upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 2
gttagagtttgatatt--tctagtaacctgtgagtatt---attttcgttcttt--ttaccagtctcttagcctagaggattactcctgattata----tgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
      |||||    |  | |   | |   ||| ||||   ||    || | |    ||  |||   ||  |   |   | ||||  | |||||     | | |  |||||||| || || || ||||| ||||| ||||||||||| || ||||| || || |||| ||| ||| | ||||||||||||||||| || |||||||| |
------gtttggagctcattttacatctcttgaatattccaatccaagtgcatgaaataagagtagatttactgtgtaaagtacttataattatggttgttattttcagGTTGAATTTATCTTAATGGGCGGTACCTTCATGTCACTTCCGGCTGATTACCGTGATTACTTTATAAGAAATCTTCATGATGCTTTGTCTGGACACACAT

upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gttagagtttgatatttctagtaacctgtgagtattat-tttcgttctttttaccagtctcttagcctagaggattactcc-tgattatatgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
                 |||| | | | || | | || | ||   || | | ||  | | | | | ||    ||  |  | |  |  |   |   ||  ||  |  |||  |  ||||| ||||||||||| ||||| ||||| |||||||||||||| || ||||| || |||| ||| | | ||||||| ||||||||||| |||||||||||||
gtttagtttgttgtctggttataatctaat-tatttatttacagttgtgcaatacatcttgatttattggtaagcatacttgtttgcatcttgtttcaatggctgcatgt-tttcagGTAGAGTTCATTTTAATGGGTGGTACCTTCATGTCACTGCCAGCCGAGTACCGTGATTACTTTACAAGGAATCTACATGATGCTTTGTCAGGACACACTT

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|301501204|gb|HO206744.1|HO206744
EST:     CAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG                         GTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTAT
genomic: CAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagttt ... tgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttttaccagtctcttagcctagaggattactcctgattatatgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT
                                  tcctgat  putative branch site (score: 3)
                                       attatatgaat  TA-rich tract