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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatattactgatgattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G25800.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatattactgatgatt---cctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                   |||   ||  |||| |    |      ||      |   | || ||  |||| |     |     | |   ||    | ||| ||||  | |||||||| || |||||||||||  | || || ||||| |||||||| ||||||||||| || |||||||| |||
-------------gtgggccaacgcttaaccaaatattatt-----aactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 6
gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatattactgatgattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
            | |  || ||   ||   |||   |  |  ||     || |  ||| |   ||  ||  |||  ||   ||| ||     |||   |||||  |||||||||| || |||||||||||  | || || ||||| || ||||| |||||||||||||| || ||||| |||
------------gtgtgtttaagcattgcacaaacactattgagctctgcacca-atattcagtggtta--acttgtg---ccttttg----tactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAG

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
---------------------------------gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatatt-actgat---gattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                                     ||   | |    || ||   | ||| |  | |  |    |   |     ||||  |   |  ||||| || | |     ||| |   ||       || ||||  | |||||||| ||||||||||||||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
---------------------------------gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatatt-actgat---gattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                                   | ||   | |    || ||   | |||||  | |  |        |     |||   |   |  ||||| || | |     ||| |   ||       || ||||  | |||||||| ||||| ||||||||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtacatgcttaagagaat-tcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatattactgatgattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                          |   ||  | | | ||| ||   | || | || |  | |   |   |   || ||  |  |||||    ||    ||  ||  |  |     |   |||||||  | |||| ||| || || ||||||||| | ||||| ||||| |||||| |||||||||||||||| ||||| || |||
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcatt--ttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|86040358|gb|DR336113.1|DR336113
EST:     GATTCTAAACCCTGAAAATTGCTATCCAGCACATTCTCCCCTGTGTGAAG                         GAGCTATCATCAGACTCTTCTCAGCATGTCAGATC
genomic: GATTCTAAACCCTGAAA-TTGCTATCCAGCACATTCTCCCCTGTGTGAAGgtacatgctt ... ctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATC
EST: gi|86040356|gb|DR336111.1|DR336111
EST:     GGATTCTAAACCCTGAAATTGCTATCCAGCACATTCTCCCCTGTGTGAAG                         GAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTT
genomic: GGATTCTAAACCCTGAAATTGCTATCCAGCACATTCTCCCCTGTGTGAAGgtacatgctt ... ctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaacgtatagttgttgcatattactgatgattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG
                    atattact  TA-rich tract