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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 5
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
          |||  |  || |  | |||||  | |  || ||||||||  || || | | |  ||||| |    |||| ||||| |||||||||||||||||||||||||||||||||||||||||  | |||||| |
---------gtgagttcgattattactctat--ttcattgcagctcaaca-atgtttattca--cttaactt---tttttcagGTAATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCGATGGGGCAGGC

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 5
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
||||||| |||        | |  | |||||  | |  || ||||||||   | || | | | |  ||        |||  |||| ||||||||||||||||||||||||||||| |||||||||||| | |||||| |
gtgagttcact------tcttattactctat--ttctttgcagctcaaca-gtttttattcacttata--------tttttagGTAATGGATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 2
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTC-ATTAGGGCAGAC-------------------------------------------
          |||  |  || |  | |||||  | |  || ||||||||  || || | | |  ||||| |    |||| ||||| ||||||||||||||| ||||||||||||||||||||||||| ||  |||||| |                                           
---------gtgagttcgattattactctat--ttcattgcagctcaaca-atgtttattca--cttaactt---tttttcagGTAATGGATATGCTTGGTACCAGCCTTTGGGATGTGTGGAATTCGATGGGGGCAGGCATAAGTATCTTTCATTCTTTTTTATGGTATCTTTTGTCACTCA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
|||||   |      || |     |   |||      |||  | |   |   |  |    |||    ||  || || || ||||||||||| |||||||| ||||| ||||||||||| ||||||||  | || ||   
gtgag---atatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatct-taattaaaatt-ttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
|| || ||   | |  | |      |   |   ||  ||| | |   | ||||||| | | ||     | ||| |||| || ||||||||||| |||||||| || |||||||||||||| |||||||| || |  ||  |
gtaagcttttcgta--tgagcctagtcacacattgagatgaatc---aggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtgagtt-tactgaagttaat-aaccattctatgctgccatggagctcaacgt-atcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
    || | ||  | |||  ||  | ||  || || |   |  || ||        | || |  |  ||||  ||    | ||  | ||||||||||| ||||||||||| || || |||||||| |||||||| |  |||||  |
gtatgtaatttacaatgagctttgttaaatatacttt--cgatattgattgtgttatcatgtacaagtaatgctataatatatacttcagGTCATGGACATGCTTGGTCCGAGTCTCTGGGATGTTTGGAATTCTTCGGGGCAATC

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------gtgagtttactgaagttaataacc----attctatgctgccatg-gagctcaa---cgtatcttgacttaatc-ttaattaaaatttt--ccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
                                         |   |||  ||   || || |      |||  |   |    |  ||| ||     || |       ||| ||     || | || ||  ||||||||||||||||||||| || || ||||||||||| ||||| || | ||| ||| |
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC

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|66915500|gb|CX102348.1|CX102348
EST:     GCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT                         GTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGG
genomic: GCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTTgtgagtttac ... aattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC
                                   tcttaat  putative branch site (score: 3)
                                               ttttcc  putative PPT
                      tatcttgacttaatct  TA-rich tract