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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttataggcaccacaatgcagtgcctgttgaaaaattacaacgacataccatttttagactgacatcttatgttgcttgtgtgcgaaaccaattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC

Basic information

species Zea mays
transcript GRMZM5G807767_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g50980.1 (Oryza sativa), 3'ss of exon 7
cttataggcaccacaatgcagtgcctgttgaaaaattacaacgacataccatttttagac-------tgacatcttatgttgct-tgtgtgcgaaaccaattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC
         |  || || |  ||| | |  || || ||||  | |||    |||||  |        |||| |||||| | | | ||||  |  ||| ||  || ||||||||||||||||| ||||| |||||||||  ||| |  |||||  | || |||||| | ||||||||||| || |||||||||||||||||||| ||||
-------ttaatacgataccatgcat-tgaaacaactacagtgtcatttttttttttaaaaaaaatgtgacttcttatatggttgtgtgcacacaacaaacactacagAATCCTTGGGAGCTTATAAACTTCTCGAGTGATGCCAAGATTCATCTTGACTCCTTCCTGTCGGTCTTCAACATTGCTGGCTTGCATGATGAGCTCTACC
















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|211020790|gb|FL433478.1|FL433478
EST:     GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACG                         AATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
genomic: GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
EST: gi|211151156|gb|FL467091.1|FL467091
EST:     GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACG                         AATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
genomic: GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
EST: gi|13557817|gb|BG549173.1|BG549173
EST:     GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACG                         AATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCA
genomic: GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCA
EST: gi|108953379|gb|EC364711.1|EC364711
EST:     GTGGCGTCAACAGCAAATTTGTGGAAAGATATGGGTTCTCATCACCAACG                         AATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
genomic: GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
EST: gi|211112501|gb|FL459338.1|FL459338
EST:     GTGGCGTCAACAGCAAATTTGTGGAAAGATATGGGTTCTCATCACCAACG                         AATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
genomic: GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
EST: gi|211112500|gb|FL459337.1|FL459337
EST:     GTGGCGTCAACAGCAAATTTGTGGAAAGATATGGGTTCTCATCACCAACG                         AATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT
genomic: GTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGAT

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: 47 (upstream exon), 45 (downstream exon)
Score: 58

ATGACGATAGATTATATGAGTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

ATGACGATAGATTATATGAGTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 6

ATGACGATAGATTATATGAGTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 81

ATGACGATAGATTATATGAGTGGCGTCAACAGCAAATTTATGGAAAGATATGGGTTCTCATCACCAACGgtatgaccac ... aattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatttttagactgacatcttatgttgcttgtgtgcgaaaccaattctgcagAATCCTTGGGAGCTCATAAATTTCTCGAGTCCTGCAACAATTCACATGGATTCCTTCTTATCGGTCTTCAATATCGCTGGCTTGCATGATGAGCTGTACC
            gactgac  putative branch site (score: 81)
     atttttaga  TA-rich tract