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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacacttaagaagagtgtgttgatttcatattatgcaaaggaccaaaatactgtcggtgtttgctaagcttacctataaatctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

Basic information

species Arabidopsis thaliana
transcript AT1G13320.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
gtacacacttaagaagagtgtgttgatttcatattatgcaaaggaccaaaa-tactgtcggtgtttgctaagcttacctat-aaatctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
            |   |  |  || |    |||||||  |  ||        | ||||   |       || || || |   || |  |   | ||||||| |||||||| || |||||||| ||  | || || ||||| |||||||| ||||||||||| || |||||||| |||
---------gtgggccaacgc-ttaaccaaatattattaactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 6
gtacacacttaagaagagtgtgttgatttcatattatgcaaaggaccaaaatactgtcggtgtttgctaagcttacctataaatctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
        ||||| |  |       | |    |||  ||   | ||||| ||    || ||| ||     |  | ||| |   | ||| | ||||||||||||||||| || |||||||| ||  | || || |||||||| ||||| |||||||||||||| || ||||| |||
--gtgtgtttaagcattgcacaaacact----attgagctctgcaccaatat----tcagtggttaacttg--tgccttt---tgtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
-------------------------------------gtacacacttaagaagagtgtgttgatttcatattatgcaaaggac-caaaatact--gtcggtgtttgctaagctta---cctataaatctacac--gtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                                      |      |||   | || |  ||   ||  | ||         |  ||  || ||   |   | ||| | | | |||    || | || | ||    | ||||||| |||||||| ||||||||||| ||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttac-aggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gtacacactta-agaagagtgtgttgatttcatattatgcaaaggaccaaaatactgtcggtgtttgctaagctta---cctataaatctacac--gtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                                          |    |  || ||| |  |   ||| |||    || | |||   |  |  |||   |   | ||| | | | |||    || | || | ||    | ||||||| |||||||| ||||| ||||| ||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgt-caattcagtaggataa-atttatatttac-aggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
--gtacacacttaagaagagtgtgttgatttcatattatgcaaagg------------accaaaatactgtcg---------gtgtttgctaagcttacctataaatctaca---------cgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
  |  |||  |||  || || |||||   |   ||||||  || |             || ||  |||| | |         |    || | ||||| |  |  | |               ||||||||| |||| ||| || || ||||| ||| | ||||| ||||| |||||| |||||||||||||||| ||||| || |||
gtgctcacgtttattaaaagagtgttt-ctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|124913184|gb|EH987058.1|EH987058
EST:     TATCCAGCACATTCTTCCCTGTGTAAAG                         GAATTATCATCAGACTCTTCTCAGCACGTCAGAT
genomic: TATCCAGCACATTCTTCCCTGTGTAAAGgtacacactt ... ctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGAT
EST: gi|116425646|gb|EG468238.1|EG468238
EST:     GCATTTTAAACCCTGAACTCGCTATCCAGCACATTCTTCCCTGTGTAAAG                         GAATTATCATC
genomic: GCATTTTAAACCCTGAACTCGCTATCCAGCACATTCTTCCCTGTGTAAAGgtacacactt ... ctacacgtagGAATTATCATC
EST: gi|116425639|gb|EG468231.1|EG468231
EST:     GCATTTTAAACCCTGAACTCGCTATCCAGCACATTCTTCCCTGTGTAAAG                         GAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTT
genomic: GCATTTTAAACCCTGAACTCGCTATCCAGCACATTCTTCCCTGTGTAAAGgtacacactt ... ctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggaccaaaatactgtcggtgtttgctaagcttacctataaatctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                              agcttac  putative branch site (score: 3)
                                      tataaatcta  TA-rich tract