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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG

Basic information

species Arabidopsis thaliana
transcript AT4G35950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
|| | | | | || | | |||||| || | | | | || || | ||| | ||| |||| || | | | | || || ||| | | || |||||||||| || ||||||||||| || || || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| |
----------attgtgtttcatgctatatatgatatta---tcttataaatatgtttat-tgataaa-gaaaaatgatcattattt-ttgcatctctt---cac-tttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaa-cagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
||| | || | | |||| |||| || || | | | ||| ||| | || ||| || | | | | | || || |||||| |||||||||| || ||||||||||| || || || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| |
------------aattgtgtttcaatgct---atatatgat--atcctcttataaatatgct---tattgagaaagaaagata-attttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatt-tccatt--ggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
| ||| ||| ||| || || | | || | |||| ||| || | ||| | | || ||||||| || | ||| ||||||||||||| ||||||||||| || || || ||||||||||||||||| ||||| || |||||||| || |||||||||||||| |
-----------------gtctcattttgtttattataaagtttggttaac---gttttttttttataaacattaggtta---acaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccata-tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
| || || ||| | || || | | || |||| || | | ||| || | || | | | ||||||| | | | ||||||||||||| ||||||||||| || || || || |||||||||||||| ||||| || |||||||| || |||||||||||||| |
------------------tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactat---ttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccata-tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG------------
| || || ||| | || || | | || |||| || | | ||| || | || | | | ||||||| | | | ||||||||||||| ||||||||||| || || || || |||||||||||||| ||||| || |||||||| || |||||||||||||| |
------------------tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactat---ttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
|| || ||| || | | | ||||| || | || | ||| || ||| || | || | | | ||| | ||||||||||||| || ||||||||||| || || ||||||||||||||||| ||||| ||||| || || ||||| |||||||||||||| |
------gaaaagaatcttccaaaaaaattaaggacttcggatcattc--ttttttttctttgataggcaaa---ggacttat-tgtttta-------tttttgaattattgg-gaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgatt-gtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
| |||| | || || | | | | | | || | ||| ||| |||||||||| ||||| |||||||| |||||||| || || ||||||||||| |||| ||| || || ||||| | ||||| ||||| |
-------------------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgtt-----catc--------aacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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|164050820|gb|ES009141.1|ES009141
EST:     TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTT-CCCACG                         GATTATGTTCCGACTGTTTTCGATAACTTTAGTG
genomic: TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTTTCCCACGgtattcatca ... attggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTG
EST: gi|164079680|gb|ES009977.1|ES009977
EST:     TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTTTCCCACG                         GATTATGTTCCGACTGTTTTCGATAACTTTAGTG
genomic: TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTTTCCCACGgtattcatca ... attggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
                    tactaaa  putative branch site (score: 1)
 tttccatt  putative PPT
 atacatactaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG