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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatccttttatcttagtcttgcatatacccccctccttatcgtgttatgcaatcacacttgttatctgttctaaataaccatttctttggtgagcacttaaccattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA

Basic information

species Zea mays
transcript GRMZM2G150772_T02
intron # 17
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 3'ss of exon 17
atatccttttatcttagtcttgcatatac----------ccccctccttatcgtgttatgcaatcaca------cttgttatctgttctaaataaccat--ttctttggtgagcacttaaccattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA
||||||||| |||| ||||| |||| |||          | |  | | |||  |||| | |||   |       | || |||  | | |    |||  |  || |||| ||| |||||||| | ||| |||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| ||||| || |
atatcctttgatctcagtctagcatctacttttcgtgtactcttttcctattttgttgtacaaattccgggtatcatggtattagctgttgccaactgtcattttttgttgatcacttaactactttgtacTATCGCTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCTAGTGCAACTGCAATAAGTATGCTTGGATGGGACAACAAAGTTCGATCTATCCTTTCTA
















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: 47 (upstream exon), 48 (downstream exon)
Score: 153

TGTGGTAGGAATATTGACAAATCAGAGGGTGCTAATTGCTTCTGCTGATCTTGATATACTATCAAGCAGCTCAACAAAGTTTGATCGTGGTCTCCCATCAatatcctttt ... cattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

TGTGGTAGGAATATTGACAAATCAGAGGGTGCTAATTGCTTCTGCTGATCTTGATATACTATCAAGCAGCTCAACAAAGTTTGATCGTGGTCTCCCATCAatatcctttt ... cattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

TGTGGTAGGAATATTGACAAATCAGAGGGTGCTAATTGCTTCTGCTGATCTTGATATACTATCAAGCAGCTCAACAAAGTTTGATCGTGGTCTCCCATCAatatcctttt ... cattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 88

TGTGGTAGGAATATTGACAAATCAGAGGGTGCTAATTGCTTCTGCTGATCTTGATATACTATCAAGCAGCTCAACAAAGTTTGATCGTGGTCTCCCATCAatatcctttt ... cattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttatctgttctaaataaccatttctttggtgagcacttaaccattttatacTATCGGTCAATGTTGTGGGTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCA
 gcacttaac  putative branch site 
                                            ccatttt  putative PPT
                                        ttaaccattttata  TA-rich tract