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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagagcaacattaccttatcttttaatcgttttggctttgatataatactgcgctatgtaatgctgatacatgcattctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA

Basic information

species Zea mays
transcript GRMZM2G466139_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g49940.1 (Oryza sativa), 3'ss of exon 13
--gtatgagagcaacattac----cttatctt---ttaatcgttttggctttgatataatactgcgctatgtaatgctgatacatgcattctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA
   | |  || ||      |    ||||| ||   |||||         ||| || || | ||| | | ||||||||| || | || |||  ||| ||||||| ||||||  |||||||| |||||||| ||| |||||| | | |||||||||||||| || || ||| ||| | |||||||| | |||  |||||| |
gtctgtaggatcattgcctctatgcttatgttctgttaatttgccatttttttatttagtgctg-gttttgtaatgctaatccttgtatt--tttggtagGTTACAAAAAAACTCTATGAACTAACATACGCATCAGAAAGAGTTGAGCAGTTTGCCATCGACAGTCTTTTGGCAATTGCTAATAAACATGGTGTGGAGA
















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|211079885|gb|FL183259.1|FL183259
EST:     TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTG                         GTTGCAAAAAGGCTCTATGATCTAACAT
genomic: TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTGgtatgagagc ... ctttttgtagGTTGCAAAAAGGCTCTATGATCTAACAT
EST: gi|211079884|gb|FL183258.1|FL183258
EST:     GGGGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAATTAAAATTG                         GTTGCAAAAAGG
genomic: TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGA-TTGgtatgagagc ... ctttttgtagGTTGCAAAAAGG
EST: gi|211079886|gb|FL183260.1|FL183260
EST:     TGTGCTGCCCCACTCTCA-GATGAAGTCAGGGGAAAAGCAGTTAGATTG                         GTTGCAAAAGGGCTCTATGATCTAACATATGCA
genomic: TGTGCTGCCC-ACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTGgtatgagagc ... ctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCA

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: 107

TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTGgtatgagagc ... ctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 29

TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTGgtatgagagc ... ctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 73

TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTGgtatgagagc ... ctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 119

TGTGCTGCCCACTCTCAAGATGAAGTCAGGGGAAAAGCAGTTAGATTGgtatgagagc ... ctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctttgatataatactgcgctatgtaatgctgatacatgcattctttttgtagGTTGCAAAAAGGCTCTATGATCTAACATATGCAACAGAAAAAATAGAGCAGTTTGCCATAGAGAGCCTTGTGGGAGTTGCTAATGAGCATACTGTGGACA
                             tgctgat  putative branch site (score: 119)
                                         cattcttttt  putative PPT
     ttgatataata  TA-rich tract