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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaactaagaggacaattattccattgagatctctgaagcaatgtttcatttgttcttaaaaatgtcaattccttatattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G76030.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------gtgagcaactaagaggacaattattccattgagatctctgaag--caatgtttcatttgt-tcttaaaaatgtcaat------tccttatattgat---agGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
                                      |    |  |||| | |   || ||  ||    |    ||  |   ||  ||  |||| | |  | | ||| | |||      | |  || || ||   |||||||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| || || ||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatg-ttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------gtgagcaactaagaggacaattattccattgagatctctgaagcaatgtttcatttgttcttaaaaatgtcaattccttatattgat--agGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
                                                                  ||| |  |   ||    |||  |  |||||| |   | ||  | |   || ||   | ||  |||| |  | || | || ||| |  ||||||||| || ||||||||||| ||||||||||| || |||||||| || || || ||||| ||||| ||||||||||||||||||||||||||||| ||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactc-tgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------gtgagcaactaagaggacaattattccattgagatctctgaagcaatgt-ttcattt-----gttcttaaaaatgtcaattccttatattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
                                                                   || |  |   || |  |||  |  |||     |  | || |||||  | ||| |     |||  |||  ||||    |  || | |||  ||||||||| || || |||||||| ||||||||||| || |||||||| || || || ||||| ||||| ||||| ||||| |||||||||||||| || ||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgattttgttg-cagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
gtgagcaa--ctaagaggacaattattc--cattgagatctctgaagcaatgtttcatttgttcttaaaaatgtcaa----ttccttatattg-atagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
|| || ||  ||| || || ||| |||    |   | | ||  | |  |   |||   || |    | | ||   ||    |||||| | ||  ||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||| || || || || ||||||||||| ||||||||||| || || ||
gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------gtgagcaactaagaggacaattattccattgagatctctgaagcaatgtttcatt-tgttcttaaaaatgtcaattccttatattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
                               |  | ||||    | | ||||      |||  || | |   || |||  |   | | ||| | |||  ||| | |   | |      |||   |||||||||||| |||||  | || || ||||| |||||||| || || || ||||| ||||| ||||||||||| || |||||||| || || ||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaatt------ttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgagcaactaagaggacaattattccattgagatc----tctgaagcaatgtttcatttgttcttaaaaat---------gtcaattccttatattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
  | ||        |      | ||||| | |  ||    |||      || ||| |    ||    | | |         |||||||    ||      |||   ||| ||||| || |||||| | || |||||||| |||||||| |||||||| ||||| || || ||||||||||| ||||| ||| | ||||| ||
--gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgcttattagtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

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|125082552|gb|EL143413.1|EL143413
EST:     GATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAG                         GAAGTACAATCAACCCCACGTGAAAGAACCTATCCTGAAGAGATGATAC
genomic: GATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAGgtgagcaact ... atattgatagGAAGTTCAATCAACCCCA-GTGAAAGAACCTATCCTGAAGAGATGATAC
EST: gi|124941646|gb|EL017981.1|EL017981
EST:     GATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAG                         GAAGTTCAATCAACCCCAGTGAAAGAACCTATCCT
genomic: GATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAGgtgagcaact ... atattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCT
EST: gi|124733039|gb|EH824441.1|EH824441
EST:     ATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAG                         GAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGA
genomic: ATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAGgtgagcaact ... atattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGA
EST: gi|124757955|gb|EH848085.1|EH848085
EST:     ATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAG                         GAAGTTCAATCAACCCCAGTGAAAGAAACCTAATCCTGAAGAGATGATACA
genomic: ATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAGgtgagcaact ... atattgatagGAAGTTCAATCAACCCCAGTGAAAGAA-CCTA-TCCTGAAGAGATGATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgaagcaatgtttcatttgttcttaaaaatgtcaattccttatattgatagGAAGTTCAATCAACCCCAGTGAAAGAACCTATCCTGAAGAGATGATACAGACAGGCATATCGACCATCGATGTCATGAATTCCATTGCTCGTGGACAGAA
                                       ttccttat  CT-rich tract
                  atttgttcttaaaaat  TA-rich tract