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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G27400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 3'ss of exon 5
gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
    ||    || || || |  || ||| ||     |||||    |  |      ||   || |||  ||   |||  ||  ||  ||||||||||||||   ||| |||||||||||| | ||  |||||||||| ||||| || ||||||||||||
----gtaagtttgtcaatac--ctttttgtatgctctttgtagagt--tcggtgatgctttgtctcatgagcaaatgatacttt--gcagCTTACATGTCCTCCCCGTGCCACATTGAGCTTATCCTGTCAGAGAAGGAAGAACCAGTGAAGAAAGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G702426_T01 (Zea mays), 3'ss of exon 5
gtatgtcttcttttctattcgactgttttta-caacgtttgtttcttcattcacattgtgctg----actctcgatttaattctatc-ttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
                        || | || | | |  || |  |||||||        |||    |   |  |||||||  |    || |||||||||||||||   ||| |||||||||||| ||||| |||||||||| |||||||||||||||||||||
------------------------gtatgtatcgaaggatggtctttcattcttgcgacactgttgaatggtatatttaatgttgctgttctgcagCTTACATGTCCTCCCCTTGCCACATTGAGCTGATTCTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G148744_T02 (Zea mays), 3'ss of exon 5
gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcg---atttaattctatc-ttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
               ||     |   ||  |  | |    ||  || |||   |  |||| || |       |||||||| |  | || |||||| ||||||||    || |||||||||||| |||| ||||||||||| |||||||||||||||||||||
--------------gtacgtatcgtattgaatgatggccattcatt-attgtaacagtgcagaatagtatatatttaattttgccgttctgcagCCTACATGTCCTCACCTTGCCACATTGAGCTGATCTTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G119169_T04 (Zea mays), 3'ss of exon 4
gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
||| |||    |     |     |   | | | | |      |    |||  ||         ||   |||   |  ||| ||  |||||||||||||||   ||| |||||||| ||  | || ||||||||||| |||||||| ||||||||||||
gtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactatttgca--------gcttaagatcctac-ctacctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
gtatgtcttcttttctattcgactgtttttacaacgtt-tgtttcttcattcacattgtgct-gactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
||| ||||   |  |||         |||| | | |   ||     |  ||||  | | |||  ||  ||  |||    ||| ||  | |||||||||||||   |||||||||||| ||| | || ||||| ||||| ||||| || ||||||||||||
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttg--cctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G37160.1 (Glycine max), 3'ss of exon 5
gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttat-gcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
|||||||     || | ||      | ||  | || |      || |  | ||||  |  ||    | ||   | | || | || | |||||||||||||||   ||||||||||||||| |||| ||||| ||||| |||||||||||||||||||||
gtatgtcactgattttgttga----tattgtcgacttaatggactactattacatgcttttg----ttgagagagtcctttttttttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G01110.1 (Glycine max), 3'ss of exon 5
gtatgtcttcttttctatt-cgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
|||||||     || | || | |    |     || |  |   | || | | || || || |||     || |    ||| | || ||||||||||||||||   ||||||||||||||| |||| || || ||||| |||||||| |||||||| |||
gtatgtcgctggttttgttgctatcactgacttaatggattactatt-acttac-ttatgttga-----gagtg---tcttttttttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G27940.1 (Glycine max), 3'ss of exon 5
gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
|||||||   | ||   ||    | || ||  || | ||  ||  ||||| |||  ||  |   | | ||     || |      ||||||||| ||||||   || |||||||| |||||||| || || || |||||||| ||||||||||| |||
gtatgtcaaatgttgagtt----ttttgttttaaggctt--tttatcatttacacggttttatttatggagactgtttt------tgcagCTTATATGTCATCTCCGTGCCACATAGAGTTGATATTATCTGAAAAAGAAGAACCTGTGAAGAAGGAG

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|47827860|gb|CK117544.1|CK117544
EST:     AGCCGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATC                         CTTACATGTCAAACCCATGCCACATTGAGTTGATTNTGTCAGAGAAAGAAG
genomic: AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATCgtatgtcttc ... tcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAG
EST: gi|124740576|gb|EH831738.1|EH831738
EST:     AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATC                         CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGT
genomic: AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATCgtatgtcttc ... tcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGT
EST: gi|125039402|gb|EL111671.1|EL111671
EST:     TATCGTGCTCATGGAAGAATCAATC                         CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAG
genomic: TATCGTGCTCATGGAAGAATCAATCgtatgtcttc ... tcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAG
EST: gi|163998110|gb|ES013540.1|ES013540
EST:     AGCCGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATC                         CTTACATGTCAAACCCATGCCACATTGAGTTGA
genomic: AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATCgtatgtcttc ... tcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGA
EST: gi|86074318|gb|DR370075.1|DR370075
EST:     AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATC                         CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAG
genomic: AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATCgtatgtcttc ... tcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAG
EST: gi|116444090|gb|EG486682.1|EG486682
EST:     AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATC                         CTTACATGTCAAACCCATGCCACATTGGGTTGATTTTGTCAGAGAAAGAAG
genomic: AGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCAATCgtatgtcttc ... tcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG
                                        ttctatctt  CT-rich tract
                                  atttaattctatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttcttttctattcgactgtttttacaacgtttgtttcttcattcacattgtgctgactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA