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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttgtaatcatattcgcctacttaattctactaagaactcgcacacacccatttttatatcttattgatgcctgacactgaaatcctattcgtatagGGTACTGTGAACAATGAAACTCTAGGATACTTCATTGGGAGAGTGTATCTTTTCCTTACTCGTCTTGGCATTGACAAGGAACGGCTGCGCTTCCGTCAGC

Basic information

species Arabidopsis thaliana
transcript AT1G29880.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 2
---------gttagtatttgtaatcatattcgcctacttaattctactaagaactcgcacacacccatttttatatcttattgatgcctgacactgaaatcctattcgtatagGGTACTGTGAACAATGAAACTCTAGGATACTTCATTGGGAGAGTGTATCTTTTCCTTACTCGTCTTGGCATTGACAAGGAACGGCTGCGCTTCCGTCAGC
         ||| |  ||    ||   | |   |    | ||  |  |      |        |   || || | | || ||  ||| |   |  |   |    || |   |||| | ||| |||||||| || || || |||||||| |||||||||||||| ||| | || |||||||| || |||||||| ||  || | ||  | || |
gtaaggttggtttggtttcaagattgaacttatcattatgatagttttttaggtttttttcttcttcttcttct-tattctttgtgctttttatgg---tgtgttttggtcagGGAATTGTCAACAATGAGACACTTGGTTACTTCATCGGGAGAGTGTATCTATTCTTGACGCGTCTTGGTATAGACAAGGACCGATTGAGGTTTAGGCAAC

upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 4
gttagt---atttgtaatcatattcgcctacttaattctactaagaactcgcacacacccatttttatatcttattgatgcctgacactgaaat---cctattcgtat-agGGTACTGTGAACAATGAAACTCTAGGATACTTCATTGGGAGAGTGTATCTTTTCCTTACTCGTCTTGGCATTGACAAGGAACGGCTGCGCTTCCGTCAGC
||| ||   | || ||   | |||  |||  ||| || |  |      | | ||| ||| | |  |  | ||| |  ||   ||| | |   ||    | || |  || |||| | ||| |||||||| || || |  ||||||||||||||||| || || ||||| || ||||||||||| ||||||||  || | || ||| | ||||
gttggttcgaattctatctagattgacct--ttatttgttttg----tttgtacaaaccaactgctccacctt-tgcatatgtgataatatgatggttcaatgctgattagGGAATTGTCAACAATGAGACACTTGCCTACTTCATTGGGAGAGTATACCTATTCCTAACACGTCTTGGCATAGACAAGGACAGGTTACGTTTCAGACAGC
















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|125032086|gb|EL104355.1|EL104355
EST:     GTCTGGCCAATCTGCCAAAAA-CTTTAGCCTTGGTGAAGCTGTTGCTAAA                         GGTACTGTGAACAATGAAACTCTAG
genomic: GTCTGGCCAATCTGCCAAAAAACTTT-GCCTTGGTGAAGCTGTTGCTAAAgttagtattt ... attcgtatagGGTACTGTGAACAATGAAACTCTAG
EST: gi|124881248|gb|EH960150.1|EH960150
EST:     TGTCTGGCCAATCTGCCAAAAAACTTTGCCTTGGTGAAGCTGTTGCTAAA                         GGTACTGTGAACAATGAAACTCTAG
genomic: TGTCTGGCCAATCTGCCAAAAAACTTTGCCTTGGTGAAGCTGTTGCTAAAgttagtattt ... attcgtatagGGTACTGTGAACAATGAAACTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacacccatttttatatcttattgatgcctgacactgaaatcctattcgtatagGGTACTGTGAACAATGAAACTCTAGGATACTTCATTGGGAGAGTGTATCTTTTCCTTACTCGTCTTGGCATTGACAAGGAACGGCTGCGCTTCCGTCAGC
                           gcctgac  putative branch site (score: 3)
                                         tcctattc  putative PPT
        atttttatatcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatttgtaatcatattcgcctacttaattctactaagaactcgcacacacccatttttatatcttattgatgcctgacactgaaatcctattcgtatagGGTACTGTGAACAATGAAACTCTAGGATACTTCATTGGGAGAGTGTATCTTTTCCTTACTCGTCTTGGCATTGACAAGGAACGGCTGCGCTTCCGTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA