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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA

Basic information

species Zea mays
transcript GRMZM2G073498_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
--------------gtaagtgttgtcttattaaaaataatgtaaccttc--aatttatcacaattctaactgttggtggttgttt--catctgcagtctttctgt-agcatttctctatcatagtctgtca---aagtagattat-------aaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
               | |    | | || || |  || |  | | | |   || |||   |  |  | ||| | |   | |||||     |  |  | |||| |  |     | |  || | |  ||   |   |  |   | ||       |   ||| |||||    |||| | ||  | || |||| ||||| ||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||  |||||||||||||||||||||||||||| |||||||| 
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgc-taatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 2
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtc-tttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatg-cacattgcact-tctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
                                                                     ||| |||| |   || |||  ||    | |     | | |    ||| || || |   | ||   || ||| || |  || || | ||   | || |  ||||| ||||||||||| ||| | ||||| ||  |||| ||| |||| || || || |||||||| || |||||||||||||| |||||  | |||||||||   
---------------------------------------------------------------------catgtgcactggcttatgtctcacagtttt----caattttcttaaggaggttttgcgcttttgtatatgttttctattgacataatgtcttctcctctctcagAAATGGTGCACAGAAGCTACTTGGCATTTTGATAGCTGTTGGTGAGGCAGTTGCATATGTTCTTTCTGGAATGTATGGTAGTGTGGGTCAACTTGGAGTG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G17950.1 (Glycine max), 3'ss of exon 2
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaa--gtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
                                                                 |||   |||   |  | ||  |    ||||   |  |   | ||   |    || ||  |     |||  ||| | ||||  ||    ||| ||  || |    ||| ||||||||||| ||| | ||||| ||| |||| ||| |||| ||||| || |||||||| || |||||||||||||| |||||  | |||||||||   
-----------------------------------------------------------------gttatgtctcacggttgtcaat----tttcctaaggaggttttgctcagtcatatatgcttccttttcctattggcattgacata---atttcatctcctctaccagAAATGGTGCACAGAAGCTACTTGGCATCTTGATAGCTGTTGGTGAAGCAGTTGCATATGTTCTTTCTGGAATGTATGGTAGTGTTGGTCAACTTGGAGTG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s2574g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
                                                                 |    | ||| |||   | |  |   |||  |||   || | |    | |||   | |     |    || | ||     ||     || | || | |  ||||||||||||||||||||| | || || |||||||| ||| |||| |||||||| |||||||| || || ||||||||||||||||| ||||||||||||   
---------------------------------------------------------------caggaataactgaagtagatttcaatttttttgctagtctaatttccttatgtaacctgt-----tctatatatatacaacaatctgattttctctgcct--ctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttac---tcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
                                                                        | | | |   |       |||||  | |  | |  |||| || |   ||||  | | | |  | | |||  |    ||   ||   |||| | |   |||||||||||||||||||| | || || |||||||| ||| |||| |||||||| |||||||| || || ||||||||||||||||| ||||||||||||   
------------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatat-atacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
                                                                 |    | ||  |||   | |  |   |||    |    | | |    | ||||  | |     |    || | ||   ||||     || | |||| |  ||||||||||||||||||||  | || || |||||||| ||| |||| |||||||| |||||||| || || |||||||||||||| || ||||||||||||   
---------------------------------------------------------------caggaataactaaagtagatttcaatttttttaggagttcaatttccttatgtagcctgt-----tctatatatatacaatgatctgattttctcttcct--ctcagGAATGGTGCACAAAAACTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGCGTTAGCCAACTTGGAGTT

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|6021123|gb|AW066051.1|AW066051
EST:     TCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
genomic: TCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttg ... ctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
EST: gi|31354034|gb|CD438391.1|CD438391
EST:     TCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
genomic: TCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttg ... ctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
EST: gi|32934776|gb|CF039588.1|CF039588
EST:     GTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
genomic: GTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttg ... ctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
EST: gi|148953951|gb|EC899337.2|EC899337
EST:     TCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT
genomic: TCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttg ... ctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA
             ttctgat  putative branch site (score: 3)
                                          cttctttactc  putative PPT
                  atttgtatt  TA-rich tract