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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattcccatacctcaaaaaccatgcatctagacaagttttacacttgaggaagtgtttattcatcaatactataatctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATGCTAGTGGTTGGCGGATGGAATTCAAGTAACACCTCTCACCTTCAGGAAA

Basic information

species Arabidopsis thaliana
transcript AT4G34350.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34350.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G027059_T01 (Zea mays), 3'ss of exon 7
--------gtaaaatt---cccatacctcaaaaacc---atgcatctagacaagttttacacttgaggaagtgtttattcatcaatactataatctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATGCTAGTGGTTGGCGGATGGAATTCAAGTAACACCTCTCACCTTCAGGAAA
        |  |||||    |  |   | | | |     |    | | ||||  |  | || ||||   | | |  || |  | |||   |    || ||||||  ||||||| || || ||| |||| ||| |||||||  ||||||| || || || ||||| |||||||||||||||||||||||||| || || ||||
tttggtttgagaaattgtctctttgagtgatagatttataattgttttgacatatgctgca-ttgactta-tatacatccgaccatatgtttgattcctcagGAAAGACAAGATGCTATGTATCAGCTGGTGAAAGAGAAAGTTGACCTTATTCTTGTTGTTGGAGGATGGAATTCAAGTAACACCTCTCATCTGCAAGAAA
















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|125247360|gb|EL261445.1|EL261445
EST:     GTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTG
genomic: GTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTG
EST: gi|125205268|gb|EL220222.1|EL220222
EST:     TTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCA
genomic: TTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCA
EST: gi|86036635|gb|DR332388.1|DR332388
EST:     ATGTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
genomic: ATGTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
EST: gi|125198667|gb|EL213621.1|EL213621
EST:     ATGTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAA
genomic: ATGTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAA
EST: gi|124983326|gb|EL056065.1|EL056065
EST:     CAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
genomic: CAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
EST: gi|125202403|gb|EL217357.1|EL217357
EST:     TATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
genomic: TATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
EST: gi|125213655|gb|EL228441.1|EL228441
EST:     GCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGA
genomic: GCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGA
EST: gi|86078647|gb|DR374404.1|DR374404
EST:     ATGTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
genomic: ATGTAAGCGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATG
EST: gi|125109911|gb|EL162129.1|EL162129
EST:     CGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAA                         GAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGA
genomic: CGGACATTTCATCAGCTTCAACACAATATGCGACGCTACTCAAgtaaaattcc ... atctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacaagttttacacttgaggaagtgtttattcatcaatactataatctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATGCTAGTGGTTGGCGGATGGAATTCAAGTAACACCTCTCACCTTCAGGAAA
                                              tctcttc  CT-rich tract
                          tttattcatcaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattcccatacctcaaaaaccatgcatctagacaagttttacacttgaggaagtgtttattcatcaatactataatctcttcagGAGCGACAAGACGCAATCTATGAGCTAGTGGAAGAGAAGATTGACCTCATGCTAGTGGTTGGCGGATGGAATTCAAGTAACACCTCTCACCTTCAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA