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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctcacatgatttcacctcatcacttattttgcaccatgcaattacatttattggttttggagtttcttcactgttctaactgtagaagtttgtatgcatttgtgtctttttggttattgactactttcttccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG

Basic information

species Zea mays
transcript GRMZM2G098078_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 7
gttagctcacatgatttcacctc---atcacttattttgcaccatgcaattacatttattggt----tttgga--gtttcttcactgttctaact-------gtagaagtttgt------------atgcatt-----tgtgtctt-tttggttattgactactttct---tccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG
||||| |  || |||       |   |||  |   | |  | |     |||   ||| |||||    |||| |  | |||| |||||||  || |       |||||   || |            || ||||     || || |  |   ||| |||  | | ||||   |  ||| ||||| ||||||||||||||||||||||||||| |||  | ||| |||||||| | || ||||| ||||||||||||||||| |
gttagtttgcacgatcatggtcctgaatctgtctctatttagctattgattttttttgttggtaatttttgtattgcttctccactgtttgaagtctgtaatgtagagcattatgctgactaatctatacattgttcatgcgtatcataaagttgttggtttccttctattttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG

upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------gttagctcacatgatttcacctcatcacttattttgcaccatgcaattacatttattggttttggagtttcttcactgttctaactgtagaagtttgtatgcatttgtgtctttttggttattgactactttcttccct-gtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG
                                              |  |||   |  | |||| |         |||     |||| | || | |||  ||  | || |  |   ||| || | ||  | |  |  |||  |   |||  | |   ||||  |  || ||| ||||||  ||   ||||||||||||||||||| ||| ||||||||| |||||  ||| |||| ||  | ||  | || || ||||| || || || |
gtcagtttttaattgtttgggatggatcattgattgcaattggccctttctccggttctatcactttgctttacttttcctctcatggagttgccttttatgtatgtgcatgtgtgtca-tggtttacttctcaagcttttgaaaaattcattttcatttgcat-ctgtctattttcttgtctcacagTCTCTACTTCCAGATTATCAGCGGCTCTTGAGTTCCATGCCTGCTCGCAGGTTGAACACATCGAAGCTTATAGAAAATAGTG
















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: 46 (upstream exon), 47 (downstream exon)
Score: 268

GGTGTTTAATATATGAACTCTTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAGgttagctcac ... ttccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 225

GGTGTTTAATATATGAACTCTTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAGgttagctcac ... ttccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 163

GGTGTTTAATATATGAACTCTTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAGgttagctcac ... ttccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 258

GGTGTTTAATATATGAACTCTTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAGgttagctcac ... ttccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagtttgtatgcatttgtgtctttttggttattgactactttcttccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG
                               tattgac  putative branch site (score: 258)
                                     ctactttcttccctgt  CT-rich tract
     tttgtat  TA-rich tract