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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttatattctcattagctgtagcttccattaataaatggtcttccttaacctatcttcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA

Basic information

species Zea mays
transcript GRMZM2G458035_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
gttggttatattctcat--tagctg-tagcttccattaata-aatggtcttccttaacctatcttcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA
|||||  ||||||||    || ||| || ||  |  | ||| | || | ||   | |  | | |  | |||| ||||  |||||| |||||||||||||| ||||||||||| ||||| || || |||||||||||||||||||||||||||||| |||| ||||||||||| || || |||
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgtttttttt--cagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA

upper sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
gttggttatattctcattagctgtagcttccattaataaatggtcttccttaacctatcttcttgtttctttttg--cagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA
||| || ||||| | || |  |||   |       |||  | |  ||     |   ||  |  | |  |||||||  |||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | ||||||||||||||||| ||  | || || |||
gtttgt-atatt-ttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA

upper sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 9
gttggttatattctcattagctgtagcttccattaataaatggtct--tccttaacctatcttcttgtt-tctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA
||| ||    ||||   |     ||      |  || ||||| | |   | |||   ||| ||  | |  |||||| |||||||||||||  | ||||| ||||| ||||| ||||| || || || || ||||| ||||||||| | |||||||| || |||||  | || || || || 
gtttgtggatttctggatgttcataaaaaaaaa-aaaaaatgctttgacctttataatatattaatctcctcttttggcagGGGAACAATACGGTATGCAAGTGTGCATGCACATTTAGGACGGACAGGAAGTAGAAGGGATGATCTCGAGTCACTAGCTTACACATTAATATTTCTCATT

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: 587

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttccattaataaatggtcttccttaacctatcttcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA
                        ccttaac  putative branch site (score: 380)
                    tcttccttaacctatc  CT-rich tract
        attaataaat  TA-rich tract