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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtaaattttactcaatttcaatacgaacatcgtcgcacttattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA

Basic information

species Arabidopsis thaliana
transcript AT4G34450.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 4
gtctgtaaattttactcaatttcaatacgaacatcgtcgcact-tattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
           ||  | ||| |  ||    || | |  |  || |   ||   |  || ||   |   ||   || |   || |     ||||||||||||| || |||||  |||||||||| |||||||| || | ||||||||||||||| ||||| ||  | || || ||||| || || |||  ||
----------gttggtgaatgttgattgttactttgcagttctctgcagtctatggatctttgaaagtgtctgtgttacatttgtt-gcagGTTATCATCGTGACCAGCTCGTTGATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCTAATGCAATAAGAGTTCTTTGCCGCATCATTGACTCAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
gtctgtaaattttactcaatttcaatacgaacatcgtcgcact-tattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
||  || | | ||  |   ||  | || |    | | |  |   | | | | ||  |  |     | | ||||  | | | | |    ||||| ||||| |||||||||||| |||||||||| |||||||| |||| ||||||||| || |||||||||||  | || || || || || || |||  ||
gttggtgactattggt---ttctactatgtggtttggcaaataatgtggaatgtggaaatgactttcatttgt--gatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 4
gtctgtaaattttactcaatttcaatacgaacatc--gtcgcacttattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
||  || ||  ||  |   |   |    |  |  |   |       | ||| || ||   |||     | ||||  | | | | |    ||||| ||||| |||||||||||| |||||||||| |||||||| ||||  |||||||| || ||||| |||||  | || || || || || || |||  ||
gttggtgaacattggttgctactatgtggttcggcaaataatgtggaatgtggggatgacttcc----atttgt--gatctattgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACCGATATGTACCGTGCAAACGCTATTAGAGTTCTTTGTCGTATTATCGACTCAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 4
-----------gtctgtaaattttactcaatttcaa---tacgaacatcgt-cgcacttattgtaggtatattttctgataagttgttggttttttcgccc-----atagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
            | || || ||||  |  |||| |     | |   || ||  |   |  || |   ||  ||   | |||| |  |   | | ||          ||||||||||||||| ||||||||||| |||||||||||||| || || ||||||||||| ||||||||||| || || || || || || || |  |||||||
gtttcattttcttatgcaacttttcttttattttagattcatgcgtatggtatgtgatctttattactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGATATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 4
-----------gtctgtaaattttactcaatttca-atac--gaacatcgtc-gcacttattgtaggtatattttctgataagttgttggttttttcgccc-----atagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
            | || || ||||| |  |||| | || |  |   || ||| |   |   |||   ||  ||   | |||| |  |   | | ||          ||||||||||||||| ||||||||||| |||||||| ||||| || || ||||||||||| ||||||||||| || || || || || || || |  |||||||
gtttcattttcttatgcaacttttattttattttatattcttgtgtatggtctgtgatctgtgttactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGACATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 4
---------gtctgtaaattttactcaatttcaa---tacgaacatcgtcgcacttattgtaggtatattttctga------taagttgttggtttt--ttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
            || || ||| |       |||     ||||| || |||     |||   |   | |  ||||||      ||  |  ||  ||||  ||       ||||||||||||| ||||||||||| |||||||| ||||||||||| | |||||||||  | || |||||||| |||||||| || || || |  || ||||
gttacaaattcttgcaattttcatgagcagtcagattcacgaatattgtc-tgtatatcacaaacagagattctgaccgttctatctcttttattttacttttttaccagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACGGATGGAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
gtctgtaaattttact---caatttcaat-acgaacatcgtcgcacttattgtaggtatattttctga------taagttgttggtttt--ttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
   |  ||||| |  |   || |   | | | ||| || |||     ||||  |   | |  ||||||      ||  |  ||   |||  ||     | ||||||||||||| ||||||||||| |||||||| ||||||||||| | |||||||||  | || |||||||| |||||||| || || || | ||| ||||
-gttacaaattctcatgaccagtcagattcatgaatatggtc-tgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtaaattttactcaatttcaatacgaacatc-gtcgcacttattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
    || || || | |    ||  ||  |    |  ||  ||  | |  | |  | |  | ||||   |||  |  ||| |   |  | ||||||| || || || ||||| || |||||||| |||||||| || | |||||||||||||||||||||||| || || ||||| || ||||  || ||||
----gttaaattgattgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttatataca-aaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtctgtaaattttactcaatttc----aatacgaacatcgtcgcacttatt-gtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
         |  | |||  |  | || |       |  ||||||  |  ||       | ||||  ||      || |       |   | |    |  |||||||||| || ||||||||| |||||||||||||||| || || |  ||  | ||||| |||||||| ||  | || || || || || | ||||||  
agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattc-cagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG

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|125212056|gb|EL227010.1|EL227010
EST:     TCATCTGATGAG                         GTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGAT
genomic: TCATCTGATGAGgtctgtaaat ... tcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGAT
EST: gi|164201597|gb|ES170545.1|ES170545
EST:     GGAGAATGGTCTACTTGATCATTAAGGAGTTATCTCCATCATCTGATGAG                         GTTATCATCGTAACAAGCTCTCTGATGAAGGATA
genomic: GGAGAATGGTCTACTTGATCATTAAGGAGTTATCTCCATCATCTGATGAGgtctgtaaat ... tcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATA
EST: gi|164206903|gb|ES050517.1|ES050517
EST:     TTGATCATTAAGGAGTTATCTCCATCATCTGATGAG                         GTTATCATCGTAACAAGCTCTCTGAT
genomic: TTGATCATTAAGGAGTTATCTCCATCATCTGATGAGgtctgtaaat ... tcgcccatagGTTATCATCGTAACAAGCTCTCTGAT
EST: gi|116437844|gb|EG480436.1|EG480436
EST:     GGAGAATGGTCTACTTGATCATTAAGGAGTTATCTCCATCATCTGATGAG                         GTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGAT
genomic: GGAGAATGGTCTACTTGATCATTAAGGAGTTATCTCCATCATCTGATGAGgtctgtaaat ... tcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgcacttattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA
                       ttctgat  putative branch site (score: 3)
                                        ttttttcgccc  putative PPT
                 tatattttctgataa  TA-rich tract