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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaacaataacatggatcacccattgttcttgtatcccatcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT

Basic information

species Zea mays
transcript GRMZM2G065012_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
---------gtgaaacaataacatggatcacccattgttc-----ttgtatcccatcattactttgaacaaacttt-----------aatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
          ||||| | |    |   |  ||   |  |      || |||       |  ||||  ||| | |||           ||| || || ||||||   |  | ||  |||||| ||||||||||| |||||||||||||| ||||| |||||||| || |||
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 9
--gtgaa-acaataacatggat-cacccattgttc-ttgtatcccatcattactttgaacaaact-ttaatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
   |  | |||   |||   |  ||  ||| |    ||||   |  | ||||        |   | || | ||     ||  |  |||     |     ||| ||||||||||| |||||||| ||||| || |||||||||||  |||  
atatatacacacacacacacacacatacatgggggattgttcacacttattatgaaatgtatgttattgaattttttctaattctaatgaatgtcac-tagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
















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|71769027|gb|DR966964.1|DR966964
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAG
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAG
EST: gi|50323441|gb|CO518567.1|CO518567
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
EST: gi|78124010|gb|DV542394.1|DV542394
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 145

AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
                  ctttaat  putative branch site (score: 145)
                                         tactcctt  putative PPT
            aacaaactttaattta  TA-rich tract