Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctttattcagacttaacttgctcgggccactttaaggaaaaaagagatgtttatttataccttgaggaaagtagggtttcatgtcttataatagcataccactgggtttgagcatgcatgtcaataacacatcaatcttatcagtgcatatgattgaatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTTGCATTTGTATACCCAGACAAGAATGGTCGTTTTGTTGTCAGACAG

Basic information

species Zea mays
transcript GRMZM2G060669_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02960.3 (Oryza sativa), 3'ss of exon 4
gtaagtcctttattcagacttaacttgctcgggccactttaaggaaaaaagagat--gttta--tttatac--cttgaggaa---------agtagggtttcat--gtcttataatagca---------taccactgggtttgagcatgcatgtcaataacacatcaatcttatcagtgcatatgattgaatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTTGCATTTGTATACCCAGACAAGAATGGTCGTTTTGTTGTCAGACAG
|||| |  | || |   | |   ||| || |  || ||||  ||||||   |  |     ||  |||||||  ||| |  ||         |  |   ||| |   |||| || ||   |         |  ||||  ||||||  |    |     | | |     |||| |||||  ||  |      || |||||||||||||||||||||||| ||||||| ||||| || || |||||||||||||| || || ||||| || ||| |||||||||| ||||||| | ||
gtaatttttctaat---attgtgctttcttgt-cctctttggggaaaatgaaattttacctagttttatactacttaacaaactagaaatcaacaaaatttgactagtctgatgatgataagtggggtttggcactacgtttgactaaatgttgtttttagatggagatctgatcagcacagttttggttatgtttcagGTGAAAGAGGTTGCTCTTGCAGCAAGAAAAAGAAATGCAAGGCTTTCTTTTGCTTTCGTGTACCCTGATAAGCATGGTCGTTTCGTTGTCAAAGAG
















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|211273990|gb|FL433152.1|FL433152
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|60394770|gb|DN227640.1|DN227640
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|20802865|gb|BQ293915.1|BQ293915
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|5608402|gb|AI901979.1|AI901979
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|9733680|gb|BE512432.1|BE512432
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|26456474|gb|CA828057.1|CA828057
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|37395737|gb|CF635151.1|CF635151
EST:     TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
EST: gi|44901460|gb|CK828005.1|CK828005
EST:     TTCAGATTTACTCATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTT                         GTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT
genomic: TTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctt ... aatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcatgtcaataacacatcaatcttatcagtgcatatgattgaatttttcagGTGAAAGAGGTTGCTCTTCCAGCAAGGAAAAGGAACGCGAGGCTTTCTTTTGCATTTGTATACCCAGACAAGAATGGTCGTTTTGTTGTCAGACAG
          caataac  putative branch site (score: 2)
                                               tttttc  putative PPT
                                    atatgattgaattttt  TA-rich tract