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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacttctagacgaaatttgtgtgtttaaaaactgatctactatgttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA

Basic information

species Arabidopsis thaliana
transcript AT4G05420.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18
gtataacttctagacgaaatttgtgtgtttaaaaactgatctactatgttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
|||| | |  |  |     |||    ||  ||    ||||   |||| |||  |   |       || |    || ||      |  |  ||||||||||| |||| ||||| ||||  ||| |||||||||||||||| ||||||   || |||||||| || ||||| || || ||  | || || ||||
gtatgattgtttaattg--tttaca-gtgcaacgtatgat--gctatattc-ctaacttccacagctaacattttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
----gtataactt--ctagacgaaatttgtgtgtttaaaaactgatctactatgttcatttggtattgtt--tctgatggcttattcttgaatgt-----aaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
    || |   ||  ||    |  || |   | |||  |   |  | |  | |||   |     ||||||  |  |   | ||  | |||  | |        |||| |||||| | || ||||| ||||| ||| |||||||||||||||| |||||| | || |||||||| || ||||||||  | ||| | || || ||||
gtgagtcttttttaactgttggcgatcttattatttgtatttttcttttttgtgtcagtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
--------------gtataacttctagacgaaatttgtgtgt-ttaaaaactgatctactatgttcatttggtattgtttctgatggcttat-tcttgaatgtaaa--agCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
               | |||||  | |    | |     ||  |||       |  || | ||| | | |  | |||   ||||| ||| || | ||   |||  |  |||| |||||| | || || || ||||| ||| |||||||||||||||| |||||| | || |||||||| || ||||||||  | ||  | || || ||||
gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctt-tgttggg-ctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 18
---------------------------------------------------gtataacttctagacgaaatttgtgtgtttaaaaactgatctac-tatgttcatttggt--attgtttc----tgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
                                                     |    |  |   |  | | | |  | | || ||||||| |   ||| |  | |  ||  ||| |||     ||||   || |||||  || | | |||| || |||||||| ||||||||  | ||||| || ||||||||||||||||||||||| ||||| ||  | |||||||| || ||||| ||||| || |
gtaaattttaaactgttgtgacactagtttctgtctggttttgttaaatttcaactgttcttctgcttagtgttttggatgaataactgatttttgtatatataatgagtacattcttttggaatgataaattgttcttttat-tgatagCATGAAGAAGGTGCTATTGAGGAAAGAGCTCGTGACTACAATGCAAATTGGATGTCAGCCGTTGAAATCGTTGATGATGACATATACCTAGGTGCAGAAA

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 18
----------------------------------------------------------------gtataac-ttctagacgaa-----atttgtgtgtttaaaaactga-tctactatgttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
                                                                |  || | || | || |||       || | ||| || | | ||| |  || |||||| ||||| ||       |||   || ||| | | ||  | |||| || |||||||| ||||||||  | ||||| || ||||||||||||||||||||||| ||||| ||  | |||||||| || || || ||||| || |
gtaaattttaaactgttgtgacactagtttctgtctggttttgttaaatttcaactgttgtgctgcttatcgttttggatgaataactgattttttgtatatataatgagtacaccatgttcttttggaat-------gataagttgttccttattg--atagCATGAAGAAGGTGCTATTGAGGAAAGAGCTCGTGACTACAATGCAAATTGGATGTCAGCCGTTGAAATTGTTGATGATGACATATATCTAGGTGCAGAAA

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------gtataacttctagacgaaatttgtgtgtttaaaaactgatctac-tatgttcatttggta--ttgtttc----tgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
                                                     |    |  |   |  | | | |  | | || ||||||| |   ||| |  | |  |||  || |||     ||||   || ||||| | ||  | |||| || |||||||| ||||||||  | ||||| || ||||||||||||||||||||||| ||||| ||  | |||||||| || ||||| |         
gtaaattttaaactgttgtgacactagtctctgtctggttttgttaaatttcaactgttcttctgcttagtgttttggatgaataactgatttttgtatatataatgagtacattcttttggaatgataaattgttctttattg--atagCATGAAGAAGGTGCTATTGAGGAAAGAGCTCGTGACTACAATGCAAATTGGATGTCAGCCGTTGAAATCGTTGATGATGACATATACCTAG---------

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 18
----------------------------------------------gtataacttctagacgaaatttgtgtgtttaaaaactgatc--tactatgttcat-ttggtattg--tttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
                                              ||||  | |      ||  |    | || |      || |   |||| |  || | ||| || ||  | |||||| | |  || ||  || |  | ||| ||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||||||||
gtaagatgactaatcttcaagtaatcccttgtccttttggcagcaagtatggcgttccctggagttaaaagagtgttgtgtttgtttgttactcttatcgtcttgttaatggatgtctgattggtcctttttttattttca-gCATGAGGAAGGTGCCATTGAAGAGCGAGCCCGTGACTACAATGCAAATTGGATGTCAGCTGTTGAGATTCTTGATGATGACATTTACCTTGGTGCTGAGA

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
----------------------------------------------------------------------------------------gtataacttctagacgaaatttgtgtgtttaaaaactgatctactat----gttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
                                                                                          ||  |||     |    ||  |  ||| || |  | |      ||    | |  |||  |  |       ||| | |    |||| |     |||  || || || || ||||||||| | ||||| || |||||||| || |||||| ||||||||||||| || ||||| || | ||| || || || || |
gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaatagtaggttgtttaatgcttgaagaaatgacctgca-ttgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctactatgttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA
                          ttctgat  putative branch site (score: 3)
                                             aatgtaaaa  TA-rich tract