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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgataacacaaaagtaccttgctattgtaacaaaggaaaaatgatgaactttcttatcatgtgaaatttttctaatggtatgtattggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G12080.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g41910.1 (Oryza sativa), 3'ss of exon 4
gatttgataacacaaaagtaccttgctattgtaacaaaggaaaaatgatgaactttcttatcatgtgaaatttttctaa--tggtatgtattggaaacac--agGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG
    |      ||   |  || |    ||    ||     || |||    |    | || || |   ||  ||||||||  ||||   | |  |    ||  ||||    || || ||||||||||| || | |||||| |||| |||| |  ||||||| ||||||||||| ||||| || ||||| |||||  ||| | || 
---gtatctctaccccatcacatgcacatgtgcacccccaaacaattcaaagagatgttgtcttaccaatcttttctaacatggtgaatttctgtggtaccaagGACTATAAAATAGCAGAAAGAATTGAGAAAGAAGGAAAAGCATGTGTAATTGTTGTGAACAAATGGGACACAATCCCAAACAAGAACCATCAGAGTACAA

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G302233_T01 (Zea mays), 3'ss of exon 8
gatttgataacacaaaagtaccttgctattgtaacaaaggaaaaatgatgaactttcttatcatgtgaaatttttc-taatggtatgtattggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG
  | || ||||  |  |  || |   | ||   ||  | ||| |   ||    ||   |   ||||  | |||  |  ||||   | |  ||| | || |||||   || |||||||| || || |||| |||||| || |  ||| |  ||||||| ||||||||||||||||| || ||||| ||||| |||| | || 
-gtatgttaac-tatgaacacatgtatgtttagacccatgaagagacatatgattgtcttgtatgttcattttaacacaatgaattcttgtggtatca-agGATTATAAAATTGCAGAGAGGATTGAAAAAGAAGGAAAGGCTTGTGTCATTGTTGTGAACAAATGGGATACAATCCCAAACAAGAACCACGAGAGTACAA

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G06150.1 (Glycine max), 3'ss of exon 8
gatttgataacacaaaagtaccttgctattgtaacaaaggaaaaatgatgaactttct-tatcatgtgaaatttttctaatggtatgtattggaaacac------agGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG
     | |      || |    |   | ||  |  |||   | | || |   | |  | |||  | | |  |||| |      ||  ||||  |    |      ||||    ||||| || ||||| ||||||| |||||||||||| ||| || | ||||||||||| |||||||||||||| || ||||||||  |||||||| 
-----gttcgtgataatgcttttatttgttacatgaaaatcagattggttttcatcatatatagtattactttttgccccacttaactatttaagtgtctgttgaagGACTACAAGATAGCTGAAAGGATAGAAAAAGAAGGGAAAGGTTGTGTGATAGTTGTAAACAAGTGGGATACAATACCAAATAAAAACCAGCAGACTGCAT

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G14170.1 (Glycine max), 3'ss of exon 6
gatttgataacacaaaagtaccttgctattgtaacaaaggaaaaatgatgaactttcttatcatgtgaaa--------tttttctaatggtatgtattggaaa------cacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG
       |  |  |  | ||| ||  | |||| |||  | ||  |  ||    |||| | | || | |||        |||| |      ||  ||||  |         | ||||    || || || ||||| ||||||| |||||||||||| ||| || | ||||||||||| |||||||||||||| || ||||||||  |||||||| 
------gttcctgattaatacttttat-ttgttacatggaaatca-aattggttttcatcttatattaaagtgttactttttgccccccttaactatttaagtgtctgttaaagGAATACAACATAGCTGAAAGGATAGAAAAAGAAGGGAAAGGTTGTGTGATAGTTGTAAACAAGTGGGATACAATACCAAATAAAAACCAGCAGACTGCAT

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 3'ss of exon 9
-------gatttgataacacaaaagtaccttgctattgtaacaaa--ggaaaaatgatgaactttcttatcatgtgaaatttttctaatggtatgtattggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG
       |   || |  || |  |||  |||  ||||||| |     | |   |  |   | || || || |  |||  |||  ||  ||           ||    ||||    | |||||| || || || |||||||||||||| || || ||| |||||||||||||||||||||| ||||| || ||||||||| |||||||| 
gcatcatggactgctttcagatgagttgctttttattgtaccccctcgaagggaaaaaatatttgctgataaaatgatgtttcactgctga---------aaattgtagGACTATAGGATTGCTGAGAGGATTGAAAGAGAAGGGAAGGGTTGCCTGATTGTTGTAAACAAATGGGATACTATACCAAATAAAAACCAACAGACTGCAA

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|125042864|gb|EL115133.1|EL115133
EST:     CTGATGTTGTTGCCCTTGTCATTGAAGCTATGGCATGCATAACAGAGCAG                         GATCTGAAGATTGTAGAAAGA
genomic: CTGATGTTGTTGCCCTTGTCATTGAAGCTATGGCATGCATAACAGAGCAGgtatctcact ... ggaaacacagGATCTGAAGATTGCAGAAAGA
EST: gi|164234420|gb|ES091853.1|ES091853
EST:     GGCATGCATAACAGAGCAG                         GATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTT
genomic: GGCATGCATAACAGAGCAGgtatctcact ... ggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTT
EST: gi|125008441|gb|EL080710.1|EL080710
EST:     TGCATAACAGAGCAG                         GATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTT
genomic: TGCATAACAGAGCAGgtatctcact ... ggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgaactttcttatcatgtgaaatttttctaatggtatgtattggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG
                            ttctaat  putative branch site (score: 2)
                    tgaaatttttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgataacacaaaagtaccttgctattgtaacaaaggaaaaatgatgaactttcttatcatgtgaaatttttctaatggtatgtattggaaacacagGATCTGAAGATTGCAGAAAGAATAGAAAGAGAAGGGAAAGGATGTCTGGTTGTTGTAAACAAATGGGATACAATACCGAACAAAAACCAAGAGACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
gatttga
- - - -taacaca
- - - - - - - - - - - - - - - -taacaaa
- - - - - - - - - - - - - - - - - - - -gaaaaat