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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

Basic information

species Arabidopsis thaliana
transcript AT4G24740.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
gtaagtactgtctgttgactttttcttcatgcatcactaatc--tgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| ||| || |  ||| |||||| | |    | | | |||    ||||  |     |     |  |     | | ||  ||| | |  | ||     | ||||  |||||||||||| ||||||||||||||||||||||||||||||||||||||||||
gtgagtcctatg-gttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
gtaagtactgtctgttgactttttc-ttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
             ||    ||  |  |||    | |||   ||||        | || |    |||  |   |   || |  | |   |||     | ||||  |||||||||||| ||||||||||||||||||||||||||||||||||||||||||
-------------gtgagtttgctggttcggttaacacccttctg-------tatgctttacattcataagattgcttgtatata---taagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 4
gtaagtactgtctgttgactttttc-ttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
             ||    ||  |  ||||   | |||  || ||       |  || ||  ||   ||||||  || |   | | | |     |||       |||||||||||| ||||||||||||||||||||||||||||||||||||||||||
-------------gtgagtttgctggttcagttagcacctatatg-------cgtgcttacgttcataagattgcttgt-atataagctggtctatt-------ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 3
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
||||||| | |    | |  |||   ||| | ||   || |   |||||              |||  |||||  ||  |||  ||||||||     |||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtaattttaacttaaatttg--tcacgtatgcatactacaatgaaaa------------tccttgattccatt--gcattggttaaatgggcttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
||||||| | |    |||   |||  | |    | |   || ||      | |   |   | ||    |||||  ||  |||  ||||||||   | |||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtattttgacctgaaacttttcttacatgttat--atatgccagtatgacataccatattt---gattccatt--gcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
||||||| | |    |||   |||  |  ||    ||    |      |||    ||||    ||   |||||   |  |||  ||||||||   | |||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtatttttacctgaaacttttct--tgttatacatgcc------agtacgacata-ccatctttgattccagt--gcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 3
gtaagtactgtctgttgactttttcttcatgcatcactaat-ctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
         ||  || || ||    |  ||   ||||  || ||  |  |  | |  ||     |||  |||||  ||  |||  ||||||||     |||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
---------gtaagtagatttaacttaaatttgtcacgtatgctagtacatactacaatgaaaatccttgattccatt--gcattggttaaatgggcttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||  |  ||  ||   ||  || | |      | | | |   | | ||    |   ||||| |||   | ||||  ||| |||||||| | | ||||| |||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
gtgagtgtttactagtgttgttaactccttaacctgccactgttg-gcactcttataagcttttctaag---cattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT

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|124929259|gb|EL006821.1|EL006821
EST:     GAAATTGAAATGCTGCAACAGCTTGGTAAACATGACAAAGGTGGCAATCG                         TTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATAT
genomic: GAAATTGAAATGCTGCAACAGCTTGGTAAACATGACAAAGGTGGCAATCGgtaagtactg ... ttccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATAT
EST: gi|125321802|gb|EL335887.1|EL335887
EST:     TGCTGCAACAGCTTGGTAAACATGACAAAGGTGGCAATCG                         TTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: TGCTGCAACAGCTTGGTAAACATGACAAAGGTGGCAATCGgtaagtactg ... ttccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
                                           tattcctt  CT-rich tract
                                ttaaatcattgtatt  TA-rich tract