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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG

Basic information

species Zea mays
transcript GRMZM2G020418_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 2
--------------------gtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                    | ||    | |||||    |    |  | ||  || | | | |||||||  | | ||  | ||  | | | ||||  ||||| ||||| || |||||| ||||||||||||||||||||||  | |||||||| || ||||| ||||||||||| ||||||||||||||||| || |||
gtgagtgcctaccgcgttttgggatccatttgtttaaagtgtttaacgattattgggat-gattggattaatcaagtcttgttggtttattattt-tagGCCTCAGGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAG

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 3
------------------------gtgagtgttg--tgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgtt--gttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                             |  |   ||  || | |        || ||  |  || ||| | || || || ||  ||||   | |||  | | ||| ||      ||| || ||| | |||||    |||||||| ||| |||| || || ||||| ||  | ||||| ||||||||||||||||||||||| || 
gtaagcttccatcctcactctttccccccttctaattgactgagtttattgcttttcccccttgttcttttggtt-ttaatctttggtttggatttgtattattcagTCCAACTCATTCTTCAGCGCTTTTCTTTCAATACAACACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAA

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtgagtgttgtgtttgcgctcggaat-----ggtttcctgtgcttgtttggattgttga--tgttgttttcttctgtgatt-tacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
               | |    | | |  ||      |||       ||| ||||| ||  |   |||||| |  | || |||  || | |||   | ||||||  | ||| |||| ||  | |||||||  |||||||| || ||||||||||| ||||||||  | ||||||||||| ||||||||||| || || |||
gtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatc--attgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP01317 (Chlamydomonas reinhardtii), 3'ss of exon 2
-----------------------------------------------------------gtgagt-gttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG------
                                                           || | | |||| |  ||| |||  |     | |   | |    |||     |   ||||| |  |  |   |   | |||   | |||| ||||||||| |||||||| ||||||||||     ||||||||||||||| |||| | ||||| |||||||| ||||| ||||| ||  ||      
gtgtgagtgcagcagcggcgctctgccctagcacgctggccacagccaaaaccctgagcgtcaatcgttgggcatgctctcacacatcatgctgctcccgacttgtcacctccctgttgctgcccacgtggtgctgcagtgagaagGTGTCGTCGGCGCTGTTCTTCCGCTACAACACGCAGCTGGGGCCGCCGTATCAGGTGCTGGTGGACACCAACTTTATCAACTTCTCCATCAAGAACAAG

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|91876075|gb|EB406032.1|EB406032
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|76018426|gb|DT945596.1|DT945596
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|50332975|gb|CO528101.1|CO528101
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|76021688|gb|DT948858.1|DT948858
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|74245267|gb|DT653181.1|DT653181
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|50330327|gb|CO525453.1|CO525453
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGNGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|78087731|gb|DV516124.1|DV516124
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|93013576|gb|EB639096.1|EB639096
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|148956652|gb|EC902508.2|EC902508
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC

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: 45 (upstream exon), 49 (downstream exon)
Score: 253

ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 118

ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                        tgttgat  putative branch site (score: 118)
                                ttgttttcttctgt  CT-rich tract
                                ttgtttt  TA-rich tract