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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G17770.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g40990.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------gtta-gccacaacattcaactttttttgcgt--ttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgt---ttttgtat-atcgtctatga---caatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
                                                    | | |||  |||  || |||||  | |     |  || | |    |   |||| |  |  |   | |    | | ||   ||| |    |     ||  |  |||  || ||    ||  |  ||||||| ||| | ||| ||||||||||||| ||||| |||| ||||||||| || || |||||||| ||||||||  |||| ||||||
gtttgttttctgttctgaggtctagtactttgtactgtggtgtgcaataatttcatgcctgaactgtctactttggtagtcccatcttctactacttactgctaatactactatattatggcttgcattaaattcctaccatgcaccttacaccatcagctttgttttcatgagcagCCTCCAGAAATCTGGAATGGTGGTGTTGGGTTTGTGTCAATGGAAATGATCCAAACCCATTGCCCGGCACCTGCTGCTGACATTCAG

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G157263_T01 (Zea mays), 3'ss of exon 7
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgt-tcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
                   |||  |||  |||| |   | ||| ||  |   |    |      |  | |    | ||| ||||  |     || ||  ||| |    |      ||||||| ||||| ||||| ||||| || || || || || ||||||||||| |||||||||||||| || |||||  | || ||||||
------------------gtttacttgtatttccc---tataattagttggtaccctactatgcttcgctcgtctgtgtgtcttactaaacatgcat--cgtttcctgcg----cagCCTCCTGAAGTCTGGGACGGTGGCGTCGGGTTCGTGTCGAAGGAAATGATCCAGACTCATTGCCCAGCGCCTGCCGCCGACATTCAG

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 7
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
              ||  |||   |  |  | || ||     ||| | | |       |    || |||  | |||| ||  ||| ||       |    |  || |      |||||||| || ||||||||||||||||  |||||||| |||||||| |||||||| || ||||||||||| || |||   |||||| ||
--------------tcttcttccataaccctactaaacctataattctttacggctatatgacttatgac-cattttttttatgtcgtcaccccttga-attcataatctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 7
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
           ||||   ||| ||        || ||     ||| | ||| |      || |  || ||  |  || || || | ||       |    | ||| |       ||||||| || ||||||||||||||||  |||||||| |||||||| |||||||| || ||||||||||| || |||   |||||| ||
----------ccatttttcttcttccataaccctgaacctataattcttaacag-----ctatgacttatgaccattctttttat-gtcacgcccttgaatttataatctctccagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACACATTGCCCTGCTCCAGCACAAGATATTAAG

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
            |||||  |     |  | |   |   |  ||     ||    | ||    ||| |  ||  |||  ||  |||  ||  ||  |   | |||       |  ||||||| |||| |||| | ||||| || || |||||||| |||||||||||  || | ||||||||||||||||||||||| ||| ||
------------attcacatcaggcta-gctctccttttacaatgttgtatgtgatgattgtttttttttatttttattttatgtaattgctgcttg--gactactctcccac-agCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG

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|47828476|gb|CK118160.1|CK118160
EST:     TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATG
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATG
EST: gi|86082325|gb|DR378084.1|DR378084
EST:     TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATT
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATT
EST: gi|163999023|gb|EL975226.1|EL975226
EST:     CCAATTACCCTGAACAATTTAAAATCTTCTATGTTT-GAACCAG                         CCTCCGGAAGTATGGGATGGT
genomic: CCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGT
EST: gi|164061039|gb|ES070852.1|ES070852
EST:     CAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATC
genomic: CAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATC
EST: gi|125301329|gb|EL315414.1|EL315414
EST:     TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCTGGAAGTAT
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTAT
EST: gi|124764010|gb|EH854140.1|EH854140
EST:     TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATGGTGGTGTTGG
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGG
EST: gi|86066425|gb|DR362182.1|DR362182
EST:     TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCCGGA-GTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGAT
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCC-GGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGAT
EST: gi|125196020|gb|EL210974.1|EL210974
EST:     CTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATT
genomic: CTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATT
EST: gi|86082753|gb|DR378512.1|DR378512
EST:     TTACTACCAATTACCNTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATT
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATT
EST: gi|164053715|gb|ES142915.1|ES142915
EST:     TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAG                         CCTCCGGAAGTATGGGATGGTGGTG
genomic: TTACTACCAATTACCCTGAACAATTTAAAATCTTCTATGTTTTGAACCAGgttagccaca ... acaatattagCCTCCGGAAGTATGGGATGGTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
  ttctgat  putative branch site (score: 3)
                       ttgtttttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG

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