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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatggcaccaactcaccgagtgatctttggcttcctttcaactgcaatgccgttgagtatctgggctaacctcgctgaaaagatgctaattctgggaactggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG

Basic information

species Zea mays
transcript GRMZM2G006429_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 2
gtagatggcaccaactcaccg--agtgatctttggcttcctttcaactgcaatgccgttgagtatctgggctaacctcgctgaaaagatgctaattctgggaactggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG
||    |  | |  | ||  |    |||   |||    |||    ||  ||  |||| || | |  ||   |||| | |       |||| |   | || |      |||||| ||| | ||||| ||||| ||||| || || || || ||||||||||||||||| |||||||| || || || || ||||||||  |||| || |||||
gtgagagagatcctcgcaatgccgttgaaacttgaaagcctg--gac--catcgccgctgtgaagatg--ttaactttg----ggggatgttg--tgtgagtgtgattgcagGGGAGGCATCAGGGACGACAGCGACGCTGGTCGTCGTCGATGGGTTCACGGTCACGGTGGCGTCTGTTGGGGACTCCAGGTGCATATTGGACACGCAGGG
















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|26560042|gb|CA832277.1|CA832277
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71314548|gb|DR793896.1|DR793896
EST:     CGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|19822432|gb|BQ048456.1|BQ048456
EST:     GACTTCCAGCGC-AGG                         GTGAGACGTCAGGAACGACGGCGACAC-TGTTG-GGTTGATGGGTTCACGG
genomic: GACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|31354352|gb|CD438709.1|CD438709
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|76281727|gb|DV021295.1|DV021295
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71331543|gb|DR802616.1|DR802616
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|50331894|gb|CO527020.1|CO527020
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|50332586|gb|CO527712.1|CO527712
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71773439|gb|DR971341.1|DR971341
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|148995556|gb|EE034750.2|EE034750
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|89106849|gb|DY577066.1|DY577066
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71428998|gb|DR810048.1|DR810048
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGGTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71438441|gb|DR819491.1|DR819491
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|78123111|gb|DV541495.1|DV541495
EST:     CGCGCTCGTCGCAAGATTCGTCAAGACAGATATTGACTTCCAGCGCAAGG                         GTGAGACGTCGGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|67032963|gb|CO461712.1|CO461712
EST:     CGCGCTCGTCGCATGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCATGAACGACGGCGACACTTGTTGTGGTTGATGCGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|211037782|gb|FL198987.1|FL198987
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACA-ACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGA
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGA
EST: gi|149079564|gb|EE168552.2|EE168552
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|94472234|gb|EB701192.1|EB701192
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|149045413|gb|EE047836.2|EE047836
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|101394557|gb|EB819213.1|EB819213
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|74233458|gb|DT641372.1|DT641372
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71448151|gb|DR829201.1|DR829201
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|21843276|gb|BQ703857.1|BQ703857
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|149108127|gb|EE292476.2|EE292476
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|26455794|gb|CA827377.1|CA827377
EST:     CGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|211035344|gb|FL198979.1|FL198979
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
EST: gi|71323567|gb|DR798450.1|DR798450
EST:     CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGG                         GTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG
genomic: CGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGG

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: 44 (upstream exon), 49 (downstream exon)
Score: 85

GCGGTGCCCGAGGGCATCAGTCGCGAGGACTGGCTACAGGCGCTGCCGCGCGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG


Block sizes: 30 (upstream exon), 40 (downstream exon)
Score: 4

GCGGTGCCCGAGGGCATCAGTCGCGAGGACTGGCTACAGGCGCTGCCGCGCGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG


Block sizes: 40 (upstream exon), 28 (downstream exon)
Score: 6

GCGGTGCCCGAGGGCATCAGTCGCGAGGACTGGCTACAGGCGCTGCCGCGCGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 28

GCGGTGCCCGAGGGCATCAGTCGCGAGGACTGGCTACAGGCGCTGCCGCGCGCGCTCGTCGCAGGATTCGTCAAGACAGACATTGACTTCCAGCGCAAGGgtagatggca ... actggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagtatctgggctaacctcgctgaaaagatgctaattctgggaactggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG
                               tgctaat  putative branch site (score: 28)
                         aaaagat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatggcaccaactcaccgagtgatctttggcttcctttcaactgcaatgccgttgagtatctgggctaacctcgctgaaaagatgctaattctgggaactggtgcagGTGAGACGTCAGGAACGACGGCGACACTTGTTGTGGTTGATGGGTTCACGGTCACTGTGGCGTCGGTGGGAGATTCTAGGTGCATTCTGGATACACAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT