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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtg-gcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
      |  ||    ||     |     |||| ||      | |       |  | || | ||| |  | ||| |   || || || ||| |     ||||||||||| ||||  ||| | || ||||| |||||||||||||||||||| ||||| |||||||| ||||||||| |||||||| | ||||  ||||| |
------gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtt---taattattatttgta----cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
      |  ||    ||     |     |||| ||       |||||    ||      |  |  | |  |    | |||||| |  ||||     ||||||||||| ||||  ||| | || ||||| |||||||||||||||||||| ||||| |||||||| |||||| || |||||||| | ||||  ||||| |
------gtttgtttcttatggcagggccttctattgg---tctatcagttttgctc---cgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtg--gcttaacaatctatatctgatgattatttcttgtttctgatct--cagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
|||||   ||||      ||||| |  |   |     |   | |  |  ||    | || | | ||  |     ||  |  | ||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||||||||||| |||||||| |||||||| ||||||||  |||||||| | ||||  ||||| |
gttagcatctgaatggaaatttatt--tccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaac---aatctatatctgatgattatttcttgtttctgatc--tcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
|||||   ||||      || ||    || |||      ||||   |     | | |      | ||  |  |  |    |  |||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||||||||| || ||||||||  |||||||| | ||||  ||||| |
gttagcatctgattgaaaatcta----ttcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
gttagaggctgaccattgatttaatattttc-tgttaaaaacttatcaccagtggcttaacaatctatatctgatgatt----atttcttgtttctgatct--cagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
|||||   ||||      ||||| |   ||   |         ||  | |  ||  || | | ||  |  |  |  ||      | ||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||| |||||||| ||||||||  |||| ||  | ||||  ||||| |
gttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
gttagaggctgaccattgatttaa---tattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatc--tcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
  | ||  ||||  |  ||  ||    | ||||    |   ||  ||  | |  ||  | ||   ||  |  |  |    |  |||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||| ||||| || ||||||||  |||||||  | ||||  ||||| |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaa--tagaagccctgtttcaat--tccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
                   |     | |||   |  ||  | |||   || |  | |  |||   | |||||||  || || ||   ||  ||   ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||| ||||| || ||||||||  |||||||  | ||||  ||||| |
------------------gtagtgcactttgaatagaagccctatt-tcaattccatcccaa---aaatctgattcttgttgctc--tttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
                   |     | |||   |  ||  | |||   || |  | |  |||   | |||||||  || || ||   ||  ||   ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||| |||||  | ||||||||  |||||||  | ||||  ||||| |
------------------gtagtgcactttgaatagaagccctatt-tcaattccatcccaa---aaatctgattcttgttgctc--tttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
gttagaggctgaccattgatttaatattttctgttaaaaactt--atcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatct--cagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG-----------------------------------------------------------------------
|| ||   ||||      || ||    ||||||      ||||  |  |  ||     |  ||||   |  |  |    |  |||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||| ||||||| || ||||| |||||  | |||| |||  |||||||| | ||||    ||| |                                                                       
gtaagcatctgattgaaaatcta----tttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gttagaggctgaccattgatttaatattttctgttaaaaacttatcacca-gtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
      |   || ||||  |   | |  ||   ||| | | |  |       || | ||||  |||| ||  ||   ||   | |  | |   ||   ||||||||||| | || ||| | || |||||||||||||||||||| ||||| || ||||||||||| ||||||||  |||||||||||||||  || || |
------gtaggatcattagtggtaaaaatttaattagatattagttgttgcatgccataac--tcta-atgggaaacttcactttaatatgctat---agGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
     ||| |||  ||||    || | ||||  ||| |    |||||   || || |  ||   ||   || |||   | ||    |          ||||||||||| | || ||| | || || |||||| |||||||||| ||||| |||||||||||||| ||||||||  |||||||||||||||  || || |
---gtaggatgaatattggc--aaaaatttc-attaga----tatcagttgttgcatgcca---taacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
gttagaggctgaccattgatttaatattttctgttaaaaactta--tcaccagtggcttaacaatcta-tatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
     ||  | |  | ||  | || | ||||   | ||   |||  | |  |   | ||  || |  | | | |||  ||| || | |||     ||   ||||||||||  | || ||| | |||||||| ||||||||||||||||| || ||||| |||||||| |||||||| || ||||| |||||||  || || |
---gtagcattaatactg--tcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatatt-ttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
gttagaggctgaccattgatttaatattttctgttaaaaactta--tcaccagtggcttaacaatctatatctgatgattattt--cttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
     ||  | |  | ||  | || | ||||  || |    |||  | |  |   | ||  || |  |   ||||||| |||||  | |||     ||   ||||||||||  | || ||| | ||||| || ||||||||||||||||| || || || |||||||| |||||||| |||||||| |||||||  || || |
---gtagcattaatactg--tcaacaatttcattttagtttttactttataacctgttttccatttca---ctgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
------gttagaggctgaccattgatttaatattttctgtta--aaaacttatcaccagt------ggct----taacaatctatat---ctgatgattatttcttgtttct--gatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
      ||| | |   |    ||  |||  | | ||||  |    ||   | | ||  ||      | ||    ||    | ||| |   ||  || ||||   || ||| |  |||  ||||| |||||| | |  ||| | |||||||||||||||||||||||||| || ||||| |||||||| ||||| ||| |||||| ||| ||||  || || |
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG

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|116461287|gb|EG503879.1|EG503879
EST:     TGCTTGCTCTGCGGTTAGATCACACGCGTGTCGTTGATATTATGCGCAAG                         GCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAAT
genomic: TGCTTGCTCTGCGGTTAGATCACACGCGTGTCGTTGATATTATGCGCAAGgttagaggct ... ctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
                                           ttctgat  putative branch site (score: 3)
                                ttatttcttgtttct  CT-rich tract
           ttaacaatctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG