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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccattatgaatgaactaatgttgagatagctatatcagttatctcatctcctccttttacattttgttctaaaaccccaacacatatttgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA

Basic information

species Zea mays
transcript GRMZM2G082181_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082181_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g47530.1 (Oryza sativa), 3'ss of exon 4
gtccatta--tgaatgaactaatgttgagatagctatatcag-ttatctcatctcctccttttacattttgttctaaaaccccaacacatatttgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA
 ||||  |  |  ||   ||    |    ||   |  ||    ||   |    | | | || |     ||||  | ||  ||  |||  |  ||||||| ||| |||||||| |||||||| || || |||||||||||||||||||||||||||||| |||||| ||||||||| || |||||||| |||||||| | ||||
-tccagaagttagattgtctgtcatcttcatgattgaattgtcttgatttgcttgcacattgtctcacttgtgtttaactcc--acattttgttgtgatgcagATACCCTTATTTTGCTGCAGTCCTGAACTTTAGTCAATATTGGGCCCTGTACTGTTTAGTAGAATGGTATACGGCTACCAAGGATGAATTGGCACATATA
















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|71770031|gb|DR967968.1|DR967968
EST:     TAGAATCTTTTGGTGTTTATTGTGATGGAGGAATTCA-TTTACGATGTGG                         GTACCCTTACTTTGCTGCTGTTTCTCA-CTTTAGTCAATATTGGGCCCTGT
genomic: TAGAATCTTTTGGTGTTTATTGTGATGGAG-AATTCAATTTACGATGTGGgtaagacaat ... tgtgattcagGTACCCTTACTTTGCTGCTGTT-CTCAACTTTAGTCAATATTGGGCCCTGT
EST: gi|78089544|gb|DV517918.1|DV517918
EST:     CTAGAATCTTTTGGTGTTTATTGTGATGGAGAATTCAATTTACGATGTGG                         GTACCCTTACTTTGCTGCTGT
genomic: CTAGAATCTTTTGGTGTTTATTGTGATGGAGAATTCAATTTACGATGTGGgtaagacaat ... tgtgattcagGTACCCTTACTTTGCTGCTGT

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: 55

GTGATCATAAAGACCCTCACAGCCACCTTATCTCTTCTTCTAGAATCTTTTGGTGTTTATTGTGATGGAGAATTCAATTTACGATGTGGgtaagacaat ... tgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

GTGATCATAAAGACCCTCACAGCCACCTTATCTCTTCTTCTAGAATCTTTTGGTGTTTATTGTGATGGAGAATTCAATTTACGATGTGGgtaagacaat ... tgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GTGATCATAAAGACCCTCACAGCCACCTTATCTCTTCTTCTAGAATCTTTTGGTGTTTATTGTGATGGAGAATTCAATTTACGATGTGGgtaagacaat ... tgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GTGATCATAAAGACCCTCACAGCCACCTTATCTCTTCTTCTAGAATCTTTTGGTGTTTATTGTGATGGAGAATTCAATTTACGATGTGGgtaagacaat ... tgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctcctccttttacattttgttctaaaaccccaacacatatttgtgattcagGTACCCTTACTTTGCTGCTGTTCTCAACTTTAGTCAATATTGGGCCCTGTACTGTCTAGTAGCATGGTATACAGCCACCAAGGACGAATTGGCTCCTATA
                       ttctaaa  putative branch site (score: 148)
           ttttacattttgtt  TA-rich tract