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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG

Basic information

species Arabidopsis thaliana
transcript AT4G16155.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
----------------------------------------------------------gtgaagagaagaaccaaaaattgaaataaaa--aaagatagttgtatatagttctggagtgacttgcgaa-gataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
                                                           || |     | |   || | || | | | |  || | ||       |   |      |  |||||  || ||| ||| ||  |||| ||   ||       ||||||||| ||| | ||||||| ||| ||||| ||||||||||| ||||| || |||||||||||||| || ||||| || ||||||||||| |||||  | |
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacat--gaactctacttttgct---acagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
---------------------------------------------gtgaagagaagaa-ccaaaaattgaaataaaaaaagata-gtt--gtatatagttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
                                              || |  ||  |  |||     |  | |||  | |  || | |  | |    ||      |  || |   ||  | |  |  |   |||    ||   |     |||||||| ||  | |||||||  || ||||| |||||||||||||| || || ||||||||||||||||| |||||||| |||||||| || |||||  | |
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 12
---gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
    |   |      ||   |  || |  |          | ||  | ||  |  | |      || |    | |  || |   || |     | |       ||| |||| ||| |||||||||  |||||||| ||||| ||||| || || || ||||||||||||||||| || || || |||||||| || || ||  |||
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactg-cagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 12
---gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
    |   |      ||   |  || |  |          | ||  | ||  |  | |      || |    | |  || |   || |     | |       ||| |||| ||| |||||||||  |||||||| ||||| ||||| || || || ||||||||||||||||| || || || |||||||               
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactg-cagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAA---------------

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 12
gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaacac--tctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
      | ||||          |   | |       | | |  || || | ||    |   || | |   | | ||  || |      | | | | |     ||| |||||||||||||||||||||| || || || ||||||||||| ||||| |||||||| || ||||| |||||||||||||| || || || || ||||
---gtcacaagacttgttctgcgctctcattttctttgggttcatttactactctgtt--tttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 12
gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaa---cactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
 | | ||||        |   |   ||         | | || || || ||||    |   |  | |   | | ||  || |    |  | | | | |     ||| ||||||| |||||||||||||| || || || ||||||||||| ||||| |||||||| || ||||| |||||||||||||| || || ||||| ||||
-tcatgagacttgttctacgctctcattttctc---tggatgcatttacttctctgtt--ttcaccagcttgacattgctaattgtcgttttatgctttcttgcagTTGATATATAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATTGCATTAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
-gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtat-atagttctggagtgacttg--cgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
  |   ||    |   ||   ||    |         |||||| ||    |||||  | |  |||    |   |  |  ||  |  |  || | ||||||    ||| |||||||||| ||||||| ||| || || || ||||||||||||||||| ||||||||||||||||| ||||| || ||||| || || || || ||||
cttcttgaccgtatttaactcttacctttttctc---tagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatg----cagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
--gtgaagagaagaac-caaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgc-gaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
   |||    |   || |  |   |    |  |     || |||||   |  |  |    || ||    |   |  |  ||| |  |  || | ||||||    ||| |||||||||||||||||| ||| || ||  | ||||| ||||||||||| ||||||||||||||||| ||||| || ||||| || || || ||  |||
tcttgaccgtattcactcttatgcttttctctaggtgcattgttgt---tgttctttacttgtctcattgtttactaactatttttaagctgttttcatg----cagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG

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|86087012|gb|DR382771.1|DR382771
EST:     AGGCAAACMCAAAGGCCCTAGCCGAAAATGAAGGAGAAGGACTCGCTAAG                         ATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGA
genomic: AGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAGAAGGACTCGCTAAGgtgaagagaa ... atgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGA
EST: gi|125092227|gb|EL150050.1|EL150050
EST:     TGAAGGAGAAGGACTCGCTAAG                         ATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGA
genomic: TGAAGGAGAAGGACTCGCTAAGgtgaagagaa ... atgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
                                     ctctcttcat  CT-rich tract
                     ataagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC