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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG

Basic information

species Arabidopsis thaliana
transcript AT5G11950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 3
------cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
        | | ||| ||| ||      |  |    | ||| |||  |  | |  | ||  ||||     ||     |  | |    ||   |    |     |||||||||||||| || || || || || ||  ||||| |||| ||||| ||||| ||||||||||||||||| |||||||| || ||  |||| |||||||
tatggttgttcttttttataatgacccctttgccatggaaataat--ttatagatgctttgatggagaaaatatgatcagtga----attgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG

upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 3
cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattg----tatggtttgtatcgtgcccctaatcttatgacttgg--gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
     | | |||     |  | |  | | | |||  |  || ||||     | |    |||| | | |    ||    |||  |||| | |||    |     ||||||||||||||  | || || || |||||| ||||| |||| ||||||||||| || ||||||||||| || |||||||| || || || || |||||||
-----gatagtagtccctttgttatgaaaaaaaattatggtgctttcaatgtcgaaaatatgatcttttaattgttagtaag-ttataatttgcctattttgacagATATCTGGTGAACCAGTTGGTGAAGTAAGAATTGTTTCAGATATGCATGAGCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTG

upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 3
cctgcgtttgtatgatttaagatcaggagagaaa-acaatgttctt--tggggattgtatggtttgt--atcgtgcccctaatcttatgacttgg--gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
        |      |||   || |  | | ||  |   || | |   || |||   |||| | | |  ||  |  |    |  || | | |||    |     ||||||||||||||  | || || || |||||| ||||| |||| ||||||||||  || ||||||||||| || | |||||| || || ||||| ||||| |
-------gtagtccctttgtcatgaaaaaaaaattatggtgctttcaatgtggaaaatatgatcttttaatttttgcttgtaagttgtaatttgtctattttgacagATATCTGGTGAACCAGTTGGTGAAGTAAGAATTGTTTCAGATATGCATGAGCCTAAAGCTGCAATGGCTCAAGGAGCTGATGCATTTATTGCTCTCCCAG

upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 3
------cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
      |||  | | | | |   |   |||  | ||| |          | ||   | || |    |  |||  ||    |||    |||  |    | |   |||||||||||  | ||||| ||||| |||||| ||||  | |||||||||||||| || |||| |||||| || |||||||| || || ||||| || ||||
tagttccctatgatggaaagtacttcaatcttgtgagcagcttggagcatgtgaacaatggactactaatatattgt---taac---atgggtaaaatggtgacagATATCTGGCCAAACTGTTGGAGAAGTAAGAATTGTGTCGGACATGCATGAGCGGAAAGCTGAAATGGCTCAAGAAGCTGATGCTTTTATTGCTCTTCCTG

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|125211916|gb|EL226870.1|EL226870
EST:     AATCATTCCCAAAGCTTTGATGCCAATTGAG                         ATATCTGGTGAGACTGTGGGAGATGTAAGA
genomic: AATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGA
EST: gi|125317571|gb|EL331656.1|EL331656
EST:     TGTACTTGGAATCATTCCCAAAGCTTTGATGCCAATTGAG                         ATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCAT
genomic: TGTACTTGGAATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCAT
EST: gi|125136641|gb|EL176671.1|EL176671
EST:     AATCATTCCCAAAGCTTTGATGCCAATTGAG                         ATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAG
genomic: AATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAG
EST: gi|19874754|gb|AU235585.1|AU235585
EST:     AATCATTCCCAAAGCTTTGATGCCAATTGAG                         ATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAG
genomic: AATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
                          ccctaat  putative branch site (score: 3)
                             taatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA