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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G46020.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 6
---------------------------gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattatta-tattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
                           | || |  | || |   ||  ||    || ||    |||  |   || |  |     |  |   |    |  || ||   || | |  |     || |||||  |   | |||| ||| | |||||||| ||| | ||||| |||||||||||||||||||| |||||||| || || || ||||||||  |||| || ||||||
gtgtggatttcttattccgttctacctgctagactt-ttgctatttcacaatattttcttttattatctcatttgcctccccatttccttttgccctgctagtaacatctttttgtggc-caccaattgaataa-atagGTTATGTCTCTGATTGCATACTTGATGGAATTTAAAGGGAATTATGGACCACATCTCATAATTGTACCGAATGCTGTCTTGGTCAACTGGAAG

upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 6
------------------------gttaaatctgttcccgatttgcagggattcctggatttactt---ttctttcgcctttggt--gaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
                          |   | |  ||| | | | || |   |  |  |||  | |   | ||| | | |||  |  |||||||        |  |  |  |||     ||| ||| ||||| |  | |||| |||||| || |||| ||||| ||||| ||||||||||||||||| || |||||||| || || || ||||||||  | || |||||||||
gtcattccttgcttattcttgtttactttctgtactcctgttattcatgatattttttattatcgtcaatgcttcctcttttcattcgaccaatggccaggaacttatttgtatgtc--tatgctatttgttgta-atagGTCATGGCATTGGTTGCGTACCTGATGGAATTTAAAGGGAATTATGGCCCTCATCTCATAATAGTGCCAAATGCTGTCTTAGTCAATTGGAAG

upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G07550.1 (Glycine max), 3'ss of exon 5
gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtac-agGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
| || ||  | |    ||||| |    |    | | |   |  |  ||| |  |            | |  || | |  ||||   ||||  |  || || |||    | |||| |||||| ||||||||||| | ||||| |||||||| || ||||| || ||||| || || || || ||||||||| |||| || ||||||
gatatattggatgtttatttgtatttgtatgggtaatacataattattcactgt------------agtacttgtgtgttccttcaataaacttatatttttttctcgctagGTCATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTGGTCAACTGGAAG

upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 6
gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
  | ||| | | |    |    | ||  | ||| |  ||     |||||   |||  ||   || || |||     |||| |  |  |    |  |  || | ||| ||||||||||||| | ||||||||  | |||||||| ||||| || ||||| || ||||| || || ||||| |||||||||||||| || ||||||
-gtgaatttctgcatattccttatggcatactgcaacta-----ctttcaaattttatgtttaacaa-ttaagggtttgtgcagtgtttgattgtttctt-tattggacagGTAATGGCATTAATTGCTTATTTGATGGAGTTCAAAGGAAACTATGGTCCACATCTTATTATTGTTCCTAATGCTGTTCTGGTAAACTGGAAG

upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S158_37V6.1 (Physcomitrella patens), 3'ss of exon 8
gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
        ||  |  | | |    |  |    |||  ||          |  |     | |   ||   |  |  |     | |   || | |    || |    ||||||||||||||||| |||||||| ||||||||||  || || || || || || ||||| || || || |||||||| ||| |||| || ||||||
-------ttgcacttg-tatattagagtattcggaagtaaaccgaagatgtttgcaaagtcttgtagtcttcttaagaagaccagtgta-tgtgtgtatggac--gtacagGTAATGGCACTTATTGCTTATCTTATGGAGTACAAGGGCAACTACGGGCCCCATCTAATTATTGTACCCAATGCCGTTATGGTTAACTGGAAG

upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S25_252V6.1 (Physcomitrella patens), 3'ss of exon 8
gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
 ||| |  | ||    | | |  |  ||  ||        |||      |  |||||| |   ||||  | |||  |  | | |   |  | | |     |   | |||||||||||||||| |||||||| || |||||||| || || || || ||||| ||  | || || || ||||| |||||| |||| |||||||||
attagaa-tatttgaaagtagatgacatgtct-------ttttagaggtgtgtttggtaat--ataatatgttagttgataccaatttg-tttgcgtgcggacctctacagGTAATGGCACTTATTGCTTATCTCATGGAGTTCAAGGGCAACTACGGACCCCACTTAATTATTGTACCCAACGCTGTTATGGTTAATTGGAAG

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|125211838|gb|EL226792.1|EL226792
EST:     TCTTGGAAAAACTGTTCAG                         GTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGATCG
genomic: TCTTGGAAAAACTGTTCAGgttaaatctg ... ttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG
                                    tactaat  putative branch site (score: 1)
                                          ttgtttt  CT-rich tract
      aataaattattatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCGCATCTCATCATCGTTCCCAATGCTGTTCTGGTGAATTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG