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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctagtttttttggaaagcatacattgccaatgcttataatatgcacattgttctggttcattatctcattctttccctgtgatgatatttatgtagttctctaattatttgatttcattatcttaatgcattttttcttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG

Basic information

species Zea mays
transcript GRMZM2G018508_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 20
gttagtctagtttttttggaaagcatacattgccaatgcttataatatgcacattgttctggttcattatctca----ttctttccctgtgatgatatttatgtagttctctaattatttgatttcattatcttaatgcattttttcttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG
                                                     ||| | |  || || || | |       | || |||  | |||||  || |  ||||   || |    || | |   | ||  | |  |||  |  | | |||||||| ||||| || |||||||| ||||||||||| ||||| || |||||||| || ||| ||||||||
----------------------------------------------------gttgctttc-tttatcatgtaaaaaagcttgtctctgcaa-gatatgcatatcattctg-gatcagc--atgtgaccttttt--tcccctttcaccaatactagGAAATCAAGTTTGAGCCCAATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG
















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|60396042|gb|DN228912.1|DN228912
EST:     TAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAACTTTATGAG                         GAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTT
genomic: TAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAACTTTATGAGgttagtctag ... cttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTT




















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), 47 (downstream exon)
Score: 168

TAGGCTCTTTGTAAAGGCTTCAGGAAGACCACAGGACATTCTGCCGAAGCTAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAACTTTATGAGgttagtctag ... cttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 123

TAGGCTCTTTGTAAAGGCTTCAGGAAGACCACAGGACATTCTGCCGAAGCTAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAACTTTATGAGgttagtctag ... cttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 101

TAGGCTCTTTGTAAAGGCTTCAGGAAGACCACAGGACATTCTGCCGAAGCTAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAACTTTATGAGgttagtctag ... cttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

TAGGCTCTTTGTAAAGGCTTCAGGAAGACCACAGGACATTCTGCCGAAGCTAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAACTTTATGAGgttagtctag ... cttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagttctctaattatttgatttcattatcttaatgcattttttcttacattagGAAATTAAGTTCGAACCCAATGTGATGTGTGAATACATTGATAACAGGCTTCTGTTCCGATCTTGCCAG
                                           ttcttac  putative branch site (score: 146)
                                       ttttttcttacatt  CT-rich tract
          taattatttgatttca  TA-rich tract