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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_T03
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|50323441|gb|CO518567.1|CO518567
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
EST: gi|71769027|gb|DR966964.1|DR966964
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAG
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAG
EST: gi|78124010|gb|DV542394.1|DV542394
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
                  ctttaat  putative branch site (score: 4)
                                         tactcctt  putative PPT
            aacaaactttaattta  TA-rich tract