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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacttatggcgtttttgactctcggtagatttttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G04460.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g32960.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------------------atacttatggcgtttttgactctcggtagatttttcatcgcataatcatttagt-tgaacctaaac---atctagctcattttcgtgtgtttt-tggttttgt--agATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
                                                                                    ||  | |    || |    ||||  || | |     |   || || |   |   ||| ||   |       | ||| | | |  | | | |  || | || |  ||||||||||||||||||||||||| ||||| || ||| | |||||||| || || || || ||||| || ||||| ||    ||||||
gtcagctctccaatttctgctctaggaacccaagttcttcgtttgtctcggtggtcaaatttgtttttccttgcacactctctttatctttaatcttctcagttctccctacaatggatgtaatatgatgaaaaaacatgatcccccatcgtgcttcgcttaatgttctctatctcgtgatcttatctagATGATGGAATGGTGGTATCAATCTGCTGAGGAAAGAATGTCAGCTCCGACTGTATATCCCCCACCCCCTCCTCCACCTCTGCCAAAG

upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
atacttatggcgtttttgactctcggtagatttttcatcgcat-aatcatt--tagttgaacctaaacatctagctcattttcgtgtgtttttggttttgt--agATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
   ||  | ||  | |   |    ||||||| |    |   || || ||    |||| ||    | |  | ||     | |||   |  |  |   ||| |  |||||||||| |||||||||||||| |||||||| ||| | |||||||| || || || || ||||| || ||||||||| | || |||
---ctattagctctatc--cctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG

upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G43700.1 (Glycine max), 3'ss of exon 5
-----atacttatggcgtttttgactctcggtagatt--tttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
     || | |   |    | ||   ||   ||| ||   || ||     ||||| | ||  || | |||  || || | |||   |      |||   ||||||||||||||||||||||||| ||||| ||||| |||||| | |||||||| ||||| || ||||| || || ||||| ||  | ||||||
taagtatgccttctggtgatatgctgctaaataggttagctttatgtgccaatcactaag--gagcataattat-taacacatcaccta----tttgaattttgtagATGATGGAATGGTGGTACCAATCTGCTGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCTCCCCCTCCTCCGCCTCCACCAAAG

upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
-----atacttatggcgtttttgactctcggtagatt--tttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
     || |||   |    | ||    |   ||| ||   || ||    | || | | ||  || | |||  || || | |||   |      |||   || |||||||||||||||||||||| || || || || |||||| | |||||||| ||||| || |||||||| || ||||||||| | ||||||
taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaag--gagcataattat-taacacatcaccta----tttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG

upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0036g01130.t01 (Vitis vinifera), 3'ss of exon 7
atacttatggcgtttttgactctcggtagatttttcatcgcataatcatttagttgaacctaaacatctagctcattttcg-tgtgtttttggttttg------tagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
    ||     |  ||  | ||  |||||  || |  ||   |     ||||        |  | |||||| |     | |   || | ||| |||         |||||||||| |||||||| ||||| ||||| || ||| | ||||||||||| || ||||| ||||| || || |||||| | ||||||
----ttgacatgagttataatcatggtaggattctgttc---ttgctgtttaacatgttttgtagatctagttttccattgacatgctattgatttgaactactcagATGATGGAGTGGTGGTACCAATCTGCTGAGGAAAGAATGTCAGCTCCAACTGTATACCCCCCACCACCTCCCCCTCCACCTCCAAAG

upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ15566 (Selaginella moellendorffii), 3'ss of exon 7
atacttatggcgtttttgactctcggtagatttttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
                                      ||||   |  |||   || |  |   |||  | |||  |  |  | |  |          ||||||||||||||||||||||||| || || ||  || |    || || ||  | || || || |||||||| || ||  | ||||||
-----------------------------------gtacgcactcttctttcactgcagtt--ccatacaactc-ctaacacgagcctc---------agATGATGGAATGGTGGTATCAATCTGCCGAGGAACGAGTCATGGCCCCTACGATATATCCCCCGCCTCCACCACCACCGCCACCAAAG

upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ38878 (Selaginella moellendorffii), 3'ss of exon 7
atacttatggcgtttttgactctcggtagatttttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
                                      ||||   || ||    || |  |   |||  | |||  |  |  | |  |          ||||||||||||||||||||||||| || || ||  || |    || || ||  | || || || |||||||| || ||  | ||||||
-----------------------------------gtacgcactctccttccactgcagtt--ccatacaactc-ctaacacgagcctc---------agATGATGGAATGGTGGTATCAATCTGCCGAGGAACGAGTCATGGCCCCTACGATATATCCCCCGCCTCCACCACCACCGCCACCAAAG

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|164209965|gb|ES063775.1|ES063775
EST:     TGCTTGACTATGCCCAAACCGGTCTAATTGCAGCAGTTTTTATCTTCAAA                         ATGATGGAATGGT
genomic: TGCTTGACTATGCCCAAACCGGTCTAATTGCAGCAGTTTTTATCTTCAAAgtaagtatcc ... ggttttgtagATGATGGAATGGT
EST: gi|19877662|gb|AU238493.1|AU238493
EST:     TGCTTGACTATGCCCAAACCGGTCTAATTGCAGCAGTTTTTATCTTCAAA                         -TGATGGAATGGTGGTATCAATC
genomic: TGCTTGACTATGCCCAAACCGGTCTAATTGCAGCAGTTTTTATCTTCAAAgtaagtatcc ... ggttttgtagATGATGGAATGGTGGTATCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
            acctaaa  putative branch site (score: 3)
               taaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacttatggcgtttttgactctcggtagatttttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - -gtttttg
- - - - - - - - - -ctctcgg
- - - - - - - - - - - - - - - - - - - - cataatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aacctaa