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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctatgtagcagattcttcccaatcataatacacatcgattctcttcccttttctttaagatttagattggttacgttcttatttaatgggaactgttctgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG

Basic information

species Arabidopsis thaliana
transcript AT1G13770.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g11500.1 (Oryza sativa), 3'ss of exon 6
---------------------gtgcctatgtag---cagattcttcccaatcataataca--catcgattctcttccct-tttctttaagatttagattggtta-----cgttcttatttaatgggaactgttctgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG
                       |  || | |    ||  || || ||| | ||| |      |  |||    |  | |  ||  | |  ||||   |||  ||      || || |||   || |  || |    ||   ||||| || ||||| ||||||||||| |||||||||||||||||||| ||| ||||||||||  |||
gtgtcaaattctcttgctaactcgaataggcaatgccatcttattgccattgatagtttgtttactgatgagataacttgcttggtcagtattttatttgtctatagggtgtactaattctttgtg--ctttcacttttcccagGGATCTAACCTTGATAGCAATGCTAAAATGTGGCGCCTAGTTGCAGACTTTATGAATGACCTTG

upper sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------gtgcctatgtagcagattcttccca--atcataatacacatcgattct----cttcccttttctttaag--atttagattggttacgttcttatttaatgggaactgttctgttctt--cagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG
                                                |  |   ||     | | ||||     ||| |  |  | || | ||||    ||||   | |  ||     | | ||  |      ||   |||||| |      | ||   |||    ||||| || || || ||||||||||| ||||||||||| |||||||| ||| ||||||||||  |||
gtactcacttttctgtactataaacactggtctcattagtgaagctttgatcagctgccattgctccttcaaggcatcgttgtgaatattggttctggaacttctgatatactttgtctagtcagcatatcagtgtctatatttattttctgttctttctttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG

upper sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G07190.3 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------gtgcctatgtagcagattcttcccaatcataatacacatcgattctcttcccttttctttaagatttagat----tggttacgttcttatttaatgggaactgttc--tgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG
                                                                |  || | | ||||| | |     |     ||   |||    | | |  |  ||   | | ||||| ||     |  ||   || |  ||   |  |   ||| |  | |  | ||||| || || || |||||||||||||||||||||||  | ||||| || |||||||||||  | |
gtctgcttctctcatacaaacatgttcctttatcttattaattttgaactgaaatgtgcaatactagctctat-gcagactgtcatatacttggattggcatatgctgtttctctcttatctaatgattttgaaataatttttgaattatatttctctttgtcttgtcccatatgttgcagGGATCAAATCTTGATAGCAATGCAAAAATGTGGCGATTGGTTGCAGATCTTATGAATGACCTAG

upper sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g00500.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------gtgcctatg--tagcagattcttcccaatcataatacacatcgattctcttcccttttctttaagat---ttagattggttacgttctt-atttaatgggaac-tgt-------tctgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG
                                                    | | ||||  |    | || ||  |  | |   |     | |      |||       || || ||   ||  | ||  |   ||| | |||| |||  ||| | |       | |  | ||||||| || |||||||| |||||||| |||||||||||  | ||||| || || ||||||||| |||
gtagactgttctttgctgttgtaatgactattagaaaatatttgtctttatttacttatggatgttgggtttttggctgtaaatgttattgtggcacactttcttagaaattcaaaatatgtttaaatgactttattcatgatttgatgataacgtatgcaaatctttactgttcagGGCTCAAACCTGGACAGCAATGCTAAAATGTGGCGATTGGTTGCAGATCTGATGAATGATCTTG

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|86069179|gb|DR364936.1|DR364936
EST:     TGAGGGATTTTACTGGGATGCTTGGAGGTATATTGTTCACATTTTATCAG                         GGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAG
genomic: TGAGGGATTTTACTGGGATGCTTGGAGGTATATTGTTCACATTTTATCAGgtgcctatgt ... tgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAG
EST: gi|19876024|gb|AU236855.1|AU236855
EST:     TGAGGGATTTTACTGGGATGCTTGGAGGTATATTGTTCACATTTTATCAG                         GGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTT
genomic: TGAGGGATTTTACTGGGATGCTTGGAGGTATATTGTTCACATTTTATCAGgtgcctatgt ... tgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTT
EST: gi|86069180|gb|DR364937.1|DR364937
EST:     TGAGGGATTTTACTGGGATGCTTGGAGGTATATTGTTCACATTTTATCAG                         GGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTT
genomic: TGAGGGATTTTACTGGGATGCTTGGAGGTATATTGTTCACATTTTATCAGgtgcctatgt ... tgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagatttagattggttacgttcttatttaatgggaactgttctgttcttcagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG
                           atttaat  putative branch site (score: 4)
                                       ctgttctgttcttc  putative PPT
                      ttcttatttaat  TA-rich tract