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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC

Basic information

species Zea mays
transcript GRMZM2G023289_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 15
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatag-tactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctct----ttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                |||        |  ||||| | | |||| ||  ||   | || | | |   ||    | | ||  |   || || || |  |||||| | |  ||    |  |||| |||||||||||||| ||||| ||||||||||| || ||||| || || ||||||||||| |||||||| |||||||| ||||| |||||||| ||||| 
--------------------------------------------------------------------------------tcattaatgttattttatggtcgctactgcctagtggttttccagttagctaaa---atattttca---ttcagtactagctctaaactgtaccttatatcctcagATTGATCAAGGAGATTCGGTCAGATGTTTCTGATGTGGTTGCCGCAGATGAGTTTGAGTATAAGGATCCTGTTGATGGTTCTGTCTCCAAGCATCAGGGT

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                                 |     |    ||   ||  |   ||| ||  |  |   |    |     ||| |||  || || |   |      || |||||| | || ||||  || |   | || ||  |  | || |     || || ||||| |||||||| |||||||| ||||||||||| || |||||||| || 
------------------------------------------------------------------------------------------------gtatctctctctccacttaatttcaaatccattcctttttacttgtatgactttcagactcacgtttttgga--taattggtcagGATTATAAAGGGAATTCATCCAGAGGTGGCAAATGTTGCAAGCGCAGATGAGTTCGAGTACAAAGATCCAGTAGATGGCTCTGTTTCAAAGCACCAAGGG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S4_12V6.1 (Physcomitrella patens), 3'ss of exon 16
gtaagtggaactttt-tcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagc--aatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
|||| |    |  |  |    ||     |  ||||||| ||    |||        ||      |  |   |  |    ||         |    |  ||| |    || | | |  ||   | |   |      | | ||  ||     | |    |   |||     ||   |||    ||| ||||||||||||||  |  |||||||| | || ||    | |||||||||||||||||| ||||||||||||||                         
gtaacttccgcactcattttgtgccactgcttctcaaattta---tttccgtgtttattgtgtggcgcattcaagc-cgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA-------------------------

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S168_70V6.3 (Physcomitrella patens), 3'ss of exon 16
gtaagtg--gaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtcca--agtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
||||||   ||| |  ||    ||||       |||  | ||  ||   |   ||| |  ||||  | || |    |  | | | | | | ||   ||| |   |  |      |||  ||| |   ||    |||| ||     || | |  | | |||  | |  |   |    ||   ||||  |||||||| ||||| |  | |||||| |||| ||    | ||| |||||||||||||||||||| ||||||||    || |||||    || ||||| 
gtaagtttcgaattcgttt---tgtagcactgcctctgatttatacgggtc--aactaattccagcaataattttctagaaaaaacga-tgcatgtaatcac--tgcttagtgtgtgcttatctttctttttccaattgc-----tgcattggtcacaactctataca---ttctgctggctcagTATGATCAAGAAGATCAGACCAGATGTTGCTGAGGTTCAAGAAGCAGACGAGTTTGAGTACAAGGACCCAGTTGACCAGTCCGTGTCTTGTCATCAGGGT

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 16
gtaagtggaactttt-tcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagc--aatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
|||| |    |  |  |    ||     |  ||||||| ||    |||        ||      |  |   |  |    ||         |    |  ||| |    || | | |  ||   | |   |      | | ||  ||     | |    |   |||     ||   |||    ||| ||||||||||||||  |  |||||||| | || ||    | |||||||||||||||||| ||||||||||||||    ||  | ||||  |||||||| 
gtaacttccgcactcattttgtgccactgcttctcaaattta---tttccgtgtttattgtgtggcgcattcaagc-cgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagagtgtgatttgtggatctgacccagCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGACCAGTCCATATCCAGCCACCAGGGT

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 14
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                                                |||    ||| ||        | ||    ||    ||     ||  |||    || ||        |||  |  |    | ||| || ||||||||  |||   |    | ||| ||||||||||||||||| |||||||||||||| || ||  | |  ||||| || 
----------------------------------------------------------------------------------------------------------------gtaagcctcagttt---tttccccaggggtgggtcttccctgacagtgt---gagcatg-------cagAATAGTGTCAGGGATTCGATCTGATGTCGCTGGTATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGA

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 14
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                                                |||    |||  |        | ||    ||    ||     ||  |||    || ||        |||  |  |   || ||| || ||||||||  |||   |    | ||| ||||||||||||||||| |||||||||||||| || ||  | |  ||||| || 
----------------------------------------------------------------------------------------------------------------gtaagcctcaggtt--ttttccccaggggtgggtcttccctgacagtgt---gagcatg-------cagAATAGTGTCGGGGATTCGATCTGATGTCGCTGGTATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGA

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|78108858|gb|DV527275.1|DV527275
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|71426274|gb|DR807324.1|DR807324
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|5296174|gb|AI782854.1|AI782854
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|211541121|gb|FL006422.1|FL006422
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|32906153|gb|CF010966.1|CF010966
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|5895776|gb|AW037022.1|AW037022
EST:     AGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: AGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|78024768|gb|DV493155.1|DV493155
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|31357336|gb|CD441693.1|CD441693
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|67020139|gb|CO448888.1|CO448888
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|32914018|gb|CF018830.1|CF018830
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTTTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|211190026|gb|FL186116.1|FL186116
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|149060808|gb|EE157260.2|EE157260
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|44900765|gb|CK827310.1|CK827310
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

AATGTCGATGCTGGGGCTGCTAAGGAGCTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

AATGTCGATGCTGGGGCTGCTAAGGAGCTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

AATGTCGATGCTGGGGCTGCTAAGGAGCTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

AATGTCGATGCTGGGGCTGCTAAGGAGCTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                 gtctaaa  putative branch site (score: 472)
                                           tctctttgtc  putative PPT
                 aacttttta  TA-rich tract