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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaactcgattcctcgttttcaactggtcgatttggcaaaacgtttgtctacttgcaaccaataggttggttgatgcgtgtgcttctgttcaaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT

Basic information

species Zea mays
transcript GRMZM2G060669_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g02960.2 (Oryza sativa), 3'ss of exon 1
gtcaactcgattcctcgttttcaactggtcgatttggcaaaacgtttgtctacttgcaaccaataggttggttgatgcgtgtgcttctgttcaaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT-
                           |||  |   ||     | |||   | |    | || ||| ||| ||  | |  |   |  | |||   |  |||| ||   |  |  |    |  | |||||| || | |  ||| |||||||||||||| | |||||| || |||||||||||| ||||||| ||||| || || 
---------------------------gtcagtc--gcttgctgattggtgattccggagcagtagattgattcgtactagctttcttcttcct-cgggcagGGCAGGGG-GAGGTCTCGTTGCGATGGCGGGAAGGGGCGAGATGCCGATGAGGCCTGTGCGGCCAGGGCCGCCGATGCAGTACCGGGGGCCTCCTCCCATG

upper sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g02960.4 (Oryza sativa), 3'ss of exon 1
gtcaactcgattcctcgttttcaactggtcgatttggcaaaacgtttgtctacttgcaaccaataggttggttgatgcgtgtgcttctgttcaaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT-
                ||   |||  ||||  |   ||     | |||   | |    | || ||| ||| ||  | |  |   |  | |||   |  |||| ||   |  |  |    |  | |||||| || | |  ||| |||||||||||||| | |||||| || |||||||||||| ||||||| ||||| || || 
----------------gtgagcaa--ggtcagtc--gcttgctgattggtgattccggagcagtagattgattcgtactagctttcttcttcct-cgggcagGGCAGGGG-GAGGTCTCGTTGCGATGGCGGGAAGGGGCGAGATGCCGATGAGGCCTGTGCGGCCAGGGCCGCCGATGCAGTACCGGGGGCCTCCTCCCATG
















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|60394770|gb|DN227640.1|DN227640
EST:     AGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAG                         AGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
genomic: AGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
EST: gi|20802865|gb|BQ293915.1|BQ293915
EST:     CGGCGAGCGCCTTCCC-TGTCAAAATCCACCCGGCGGCAGAGCAG                         AGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
genomic: CGGCGAGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
EST: gi|26456474|gb|CA828057.1|CA828057
EST:     AGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAG                         AGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
genomic: AGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
EST: gi|37395737|gb|CF635151.1|CF635151
EST:     AGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAG                         AGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA
genomic: AGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 360

CTGCCCTCCCCACGTCCACCTCTCTCCGCCGAAGAATCGGCGGCGGCGGCGGCGGCGGCGAGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 270

CTGCCCTCCCCACGTCCACCTCTCTCCGCCGAAGAATCGGCGGCGGCGGCGGCGGCGGCGAGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 300

CTGCCCTCCCCACGTCCACCTCTCTCCGCCGAAGAATCGGCGGCGGCGGCGGCGGCGGCGAGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 205

CTGCCCTCCCCACGTCCACCTCTCTCCGCCGAAGAATCGGCGGCGGCGGCGGCGGCGGCGAGCGCCTTCCCTTGTCAAAATCCACCCGGCGGCAGAGCAGgtcaactcga ... aaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctacttgcaaccaataggttggttgatgcgtgtgcttctgttcaaactcgcagAGCCTCGTTGCTGAGGAGGGGAGATGGCAGGCATGACCGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGAT
                      ggttgat  putative branch site (score: 205)