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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaatcttttcacaattatcatcaatcaatctcttattctctatcccttcgatattgatgtaacaaatctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG

Basic information

species Arabidopsis thaliana
transcript AT5G62530.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA05G01300.1 (Glycine max), 3'ss of exon 14
------------------gcaaatcttttcacaattatcatcaatcaatctcttattctctatcccttcga--tattgatg---taacaaatctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG
                  | ||   || |||  | | |  |  ||   | ||   |||| ||||   | |   |||| |||    |||| || | ||||||||||  | || || ||||| ||||| ||||| |||||||| ||||||| ||| ||||| ||||||||||||||||| ||
atgagtttgatatcttctgaaatatttatcatgaatgtgctttatttgtgtcaggttctttatctgatgggattatttatgattaaacacatatttgcagGAAGTTGTTGGCAATTCAGTAAATGGTACTACTTATGCTGGTCTAAGAGCAAGGACAACCGGAGCTCCTCAGAATCATTG

upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA17G10610.1 (Glycine max), 3'ss of exon 14
---------------------gcaaatcttttcacaattatc-atca-atcaatctcttattctctatcccttcgatattgatgtaacaaatctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG
                      |||    || |     |    | || || | | | ||||  |||         ||  ||||  ||||  | | |||||||||| || || || ||||| ||||| ||||| ||||||||  |||||| ||| || || |||||||| |||||||||||
agttatggctgacacttatatccaacatgttacttgtctgctgagcacataattgtgttatcttctgatgtggtcattgtgattaaacacgtatttgcagGAAGTCATTGGCAAATCAGTAAATGGTACTACTTATGCTGGTTTAAGAGCAAGGACGACCGGAGCTCCACAGAATCACTG

upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA05G01290.1 (Glycine max), 3'ss of exon 14
--------------------------------------------------------------------------------------------------------gcaaatcttttcacaattatcatcaatcaatctcttattctctatcccttcgatattgatgtaacaaatctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG
                                                                                                        || | |  | |    |  | ||| ||| | | |  |||  |||         ||  ||||  ||    | | |||||||||| || ||  | ||||| ||||| ||| | ||||||||  |||||| ||| ||||| |||||||| |||||||||||
gtttattctacataatatgatatgatatcaatcgcctgcaagattttttgtggtaattagagttcaactccaaaattgagatggctgacacttatattcaacatgctacttgtctgctgagca-cat-aataagtgtgctatcttctgatttgatcattgtgattaaaaccttatttgcagGAAGTCATTGGCCAATCAGTAAATGGTACTGCTTATGCTGGTTTAAGAGCAAGGACAACCGGAGCTCCACAGAATCACTG

upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 14
------------------gcaaatcttttcacaattatcatcaatcaatctcttattctcta-tcccttcgatattgatg--taacaaatctg--tgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG
                  || | |    |   |  | | || ||      |  | |  || | |   |||||  ||  |   |   ||| | |  || ||||||| || ||||| |||||||| |||||||| |||||||||||||| | ||||||||| |||||||| |||||||||||
tagttggcatatttccaagctatttccgttgtaggtttaatgaaatggattgctgtattcaaattgtttcgaacttatttcttgtaaaacccggttgtagGAAGTGATTGGGAAATCAGTGAACGGGACTACTTATGCTGGACTAAGGGCAAGAACAACAGGAGCTCCACAGAATCACTG

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|116454778|gb|EG497370.1|EG497370
EST:     ACGCTCATCTAACTGCAGCTGTTGTTTCAAACGATCCCATCTTTCTTCAG                         GAAGTAATAGGGAACTCAGTGAATGGGACTGCATATGCTGGACTAAGAGGA
genomic: ACGCTCATCTAACTGCAGCTGTTGTTTCAAACGATCCCATCTTTCTTCAGgcaaatcttt ... atctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatcaatctcttattctctatcccttcgatattgatgtaacaaatctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG
                                    atgtaac  putative branch site (score: 3)
                              atattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaatcttttcacaattatcatcaatcaatctcttattctctatcccttcgatattgatgtaacaaatctgtgcagGAAGTAATAGGGAACTCAGTGAATGGGACTACATATGCTGGACTAAGAGGAAGAACAACTGGAGCTCCTCAGAATCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC