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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcagcacatctcagttggtgcacaccacaccacactagaagaaattcagttgccacatttagtcgtatcttaagctaaagctaatgtctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC

Basic information

species Zea mays
transcript GRMZM5G830545_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830545_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g65660.1 (Oryza sativa), 3'ss of exon 5
gtcagtcagcacatc-tcagttggtgcacaccacaccacactagaagaaattcagttg---ccacatttagtcgtatcttaagctaaagctaatgtctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC
    ||||| ||||| | |||| ||        | |   | || || |   | ||| |    |||  | |      |||||| |    |   || ||| || |||||| ||||| ||||| || |||||  |  | ||||| |||    |||||||||||||||||||||||||||||| ||||| ||||||||| | | | ||||
----gtcagtacatcataagttcgtaactgagccccggtagtaaaatattattagtagagatcaccgtgaaattattcttaaaccgg-gtgcatttctgaatgcagGTTTATGCACAGCCCATATTTGCGACAATGGAGAGATGGATCTCCTCCCGGTGGCCGGAGGCCAAGTTCATCAACAGCGAGTACACCGTAAACGTGCCGC
















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|148982433|gb|EE028314.2|EE028314
EST:     TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAG                         GTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
genomic: TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
EST: gi|91051424|gb|EB161842.1|EB161842
EST:     TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAG                         GTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
genomic: TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
EST: gi|71762914|gb|DR960851.1|DR960851
EST:     TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAG                         GTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
genomic: TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
EST: gi|89250248|gb|DY622034.1|DY622034
EST:     TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAG                         GTATATGCGCAGCCTATCTTTGTTTCGGTTGAGAGGTGGGCTGCCTCCCGG
genomic: TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
EST: gi|149007853|gb|EE040282.2|EE040282
EST:     TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAG                         GTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG
genomic: TCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGG

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: 32 (upstream exon), 30 (downstream exon)
Score: 2

TGCTCCGGGCAACATCCTGACGGCAGGCGGGTTGGGTCCCTTCTGGCTCGTCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 25

TGCTCCGGGCAACATCCTGACGGCAGGCGGGTTGGGTCCCTTCTGGCTCGTCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC


Block sizes: 42 (upstream exon), 41 (downstream exon)
Score: 15

TGCTCCGGGCAACATCCTGACGGCAGGCGGGTTGGGTCCCTTCTGGCTCGTCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 15

TGCTCCGGGCAACATCCTGACGGCAGGCGGGTTGGGTCCCTTCTGGCTCGTCGACATTGCCAACATGTGCCTCATCCTCCACCTGATCGGTGCATACCAGgtcagtcagc ... ctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcagttgccacatttagtcgtatcttaagctaaagctaatgtctcaacgcagGTATATGCGCAGCCTATCTTTGCTTCGGTTGAGAGGTGGGCTGCCTCCCGGTGGCCGGAGGCCAAGTTCATCAGCAGCGCGTACACCGTCAGCATCCCGC
                                    agctaat  putative branch site (score: 15)
                       tatcttaa  TA-rich tract