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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttgggcgaaatgtgcatagtgtttttgtcattcattctctaagaggtattttatgttggatgcatagttgacatctccttgacagaaaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCTGGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTAC

Basic information

species Arabidopsis thaliana
transcript AT2G39810.1
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G41590.1 (Glycine max), 3'ss of exon 2
tctgttgggcgaaatgtgcatagtgtttttgtcattcattctctaagaggtattttatgttggatgcatagttgacatctccttgaca-gaaaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCTGGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTAC
    ||  |     | | | |  |  |  |  ||||  |  | |  |   ||||      | |   |    ||  ||| | ||||||  |||| || | ||| |||||  |||| ||||||||||| || ||||| || |||||||| |||||||| || ||| |||||||||| || || |||||||||  |||| | ||
-aaattaagttggtttttcttctttatcctcccatttttcttatttgtcctattgcccccttgtctccacttttgcattttcttgacctgaaattttacagACATCACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATCCTGTCATTGCATTTTTGTTGGATGAAGTGGTAGTGAAGGATTGGTGCAAGAGGAC

upper sequence: AT2G39810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G03840.1 (Glycine max), 3'ss of exon 2
---tctgttgggcgaaatgtgcatagtgtttttgtcattcattctctaagaggtattttatgttggatgcatagttgacatctccttgac-agaaaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCTGGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTAC
   | | ||   |   ||   |  | | || || |   ||||  | |      | | |     | |   |    ||  ||| | |||||| ||||| || | ||| |||||  |||| ||||||||||| || ||||| || |||||||| ||||| || || ||| |||||||||| || || |||||||||  |||| | ||
tttttttttcttctttatcctcccaattttcttattggtcatattgttc----tgtctgtcacttgtctccgctttcgcattttcttgaccagaaattttacagACATCACTGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATCCTGTCATAGCATTTTTGTTGGATGAAGTGGTAGTGAAGGATTGGTGCAAGAGGAC

upper sequence: AT2G39810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0299g00030.t01 (Vitis vinifera), 3'ss of exon 1
---tctgttgggcgaaatgtgcatagtgtttttgtcattcattctctaagagg--tattttatgttggatgcatagttgacatctccttgacagaaaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCTGGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTAC
   | |   |   || || |  ||     |||| |  |  |||   ||| | |  |  ||||| || || |  ||  |    | ||||| |||||| || || |||| | ||  |||| |||||||| || |  ||||| || |||||||| ||||||||||| ||| |||||||||| |||||||| ||||||  |||||| ||
tgttatagagtctgagatct-tatgacaattttctgctatatttgttaaaaagatttctttatattagaagtctacat----tttccttaacagaagatgaacagATGTTACAGATGTTTGTATGGACGAAAGTGCTGTCTCCAGTGATCCTGTCATTGCTTTTTTGTTGGATGAAGTGGTTGTCAAAGATTGGTGCAAGCGGAC

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|19875888|gb|AU236719.1|AU236719
EST:     TCTGNTTGATGNTGCTATGAACAATAATTTGATCTCGGTGGGTTGCCATT                         ATATCACCAATGTCTGNATGGATGAGACAGCTG-ATCTAGTGATCC
genomic: TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATTgtatccttca ... aaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCC
EST: gi|116394345|gb|EG436937.1|EG436937
EST:     TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATT                         ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA
genomic: TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATTgtatccttca ... aaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA
EST: gi|116394328|gb|EG436920.1|EG436920
EST:     TCTGGTTGATGGTGCTATGAACAATAATTTGATCTCGGTGGTTTGGCATT                         ATATCACCCATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCCGTCA
genomic: TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATTgtatccttca ... aaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA
EST: gi|116394338|gb|EG436930.1|EG436930
EST:     TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATT                         ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA
genomic: TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATTgtatccttca ... aaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA
EST: gi|116394354|gb|EG436946.1|EG436946
EST:     TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATT                         ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA
genomic: TCTGTTTGATGTTGCTATGAACAATAATTTGATCTCGGTGGTTTGCCATTgtatccttca ... aaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaggtattttatgttggatgcatagttgacatctccttgacagaaaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCTGGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTAC
                                 ctccttgac  putative branch site 
                                        acagaaaattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttgggcgaaatgtgcatagtgtttttgtcattcattctctaagaggtattttatgttggatgcatagttgacatctccttgacagaaaattaatagATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCTGGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - gtttttg