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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG

Basic information

species Zea mays
transcript GRMZM2G174312_T01
intron # 2
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

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: 412

GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 240

GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 297

GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 239

GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                        tgttgat  putative branch site (score: 239)
                                ttgttttcttctgt  CT-rich tract
                                ttgtttt  TA-rich tract