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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG

Basic information

species Arabidopsis thaliana
transcript AT3G29160.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 4
------gtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
       | | |  ||| |||    |   | | | | | |  | |       |   |    | | | || | | | |  ||| | |   | |||  || |||| || || ||||||||||||||||||||||| || ||||||||||| || ||||| ||  | || |||||  | || ||||||||||| ||||||||||
gtttttttttttttttttgtatcactgtgggactatatctt-cttgctcctttgcatgcaatattttttcttattatagtat-tatggttcctt--tgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 4
gtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
|||| |  ||| |||    |     | | | | |  | |       ||  |    | | | || | | | |  ||| | |     |||  || |||| || || |||||||||||||||||||| || || ||||||||||| || ||||| ||  | || |||||  | || ||||||||||| |||||||| |
gtatttttttt-gtatcactgtgagactatatctt-cttgctcctttacatgcaatattttttcttattatagtat-tatggtccctt--tgcagGTGATCTCTGGTAAATTATATGCTGGACCCGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACG

upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
-------gtatatagtttagtaaagttactgaattg---tttttcacctatgtgactatgtctcgtttctctt-----atgagt-gtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
        | |||| |     |||| ||   |   |     ||  | |  | || |  | | || |  | |||         |  ||    | || |  |  ||  || |||| ||||| |||||| ||||||||||||||||||| ||||| ||||| || || |||||  | || ||||| ||||| |||||||| || |||||||| |
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG

upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
gtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatga-gtgtcttatctcttact-----tcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
     || |||| |    || |||     ||  | | |||| |   | | ||   |||     |  | || ||||    | || |     |  | ||| |||| ||||| |||||| |||||||||||||||| || |||||||||||||| || || ||  | || |||||  | || || |||||||| ||||||||||
----gtattttattcttattgctgtgagtttgctgatctattt--ttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG

upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
------------------------------gtatatagtttagtaaagttactga-attgttttt-------cacctatgtgactatgtctcgtttctcttatgagtgtcttatctc-------ttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
                              | ||||  || | ||| |||| |   ||| || ||        || | || |||| |   |       ||| ||| |     |||          |  |  || |   ||||||| || || ||||| ||||||||||| ||||||||||| ||||| || || || || || || |||||  | || || |||||||||||||||||||
gtttgtaaataattaaattgtaacggaataggatattatt-attaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 5
gtatatagtttagtaaagttactgaattgtttttcacc-tatgtgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
|| | || |  | || |       |||| || || |   ||| |   | ||| | || | ||||      ||   |  | ||  || ||     ||||||| || || ||||| ||||||||||||||||| ||||| ||||| || || || || || || || ||  | || || || ||||||||||||||||
gtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgt-gtgtgtcttg-----gttacactttttcattttt--cacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATG

upper sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------gtatatagtttagtaaagttactgaattgtttttcacctatg-tgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
                                        | | | ||| ||  | |      |||  ||| | |  |||| |||  |||  |    | |||    |  ||  ||  |  |    | | || ||||||||||| || | ||| || || |||||||| || ||||||||||| ||||| ||||| |||||||||||  | || ||||||||||| ||||||||||
gtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagttacaatactttctaatatatgatgataatggttgaaatttct----aaggttctaattagtgtcccattttatagGTTATATCTGGAAGATTGTACGCAGGACCTGAGGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG
                                    ctcttac  putative branch site (score: 3)
                              tcttatctcttacttc  CT-rich tract