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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagcttcagaagttttgggttaaagagtctgctacttttttttccttgtgtactctgcataatgttattcatttcttcttttggtgctgttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG

Basic information

species Zea mays
transcript GRMZM2G064753_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064753_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 3
--cttagcttcagaagttttgggttaaagagtctgcta-cttttttttccttgtgtactctgcataatgttattcattt-cttcttttggtgctgttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG
  || | |    | |  ||   ||       | |  || |||       | | ||  | |    | |||||||||||    ||  | ||||| |   |||||||||||  ||| ||||  |||| ||||||||||||||| ||||||| || || ||||||||||| ||||
atctgaaccatggcacatt--agtctcttcatttattatcttgcagcatcatttgagcaccatgtcatgttattcatcaatttgctatggtgtta--cctgcagGAGGCCCCAGCTGTCATTGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAG

upper sequence: GRMZM2G064753_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G15640.1 (Arabidopsis thaliana), 3'ss of exon 3
-------cttagc-ttcagaagttttgggttaaagagtctgctacttttttttccttgtgtactctgcataatgttattcatttcttcttttggtgctgttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG
          ||  ||||     ||| || || | | |  | ||||| ||||| | | |      | || ||    |||    | |  |||||    | || |   |||| |  ||  || | ||  ||||||||||| ||||||| || || ||||||||||||||||| || |
ttgagtgagcagtattcattttcttttggctacacaattggatacttattttttcattttcttgatacacaa----atttggatgtcattttg----tattgccttagGAAGCTCCTGCTATTGTGAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG
















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|211282257|gb|FL038859.1|FL038859
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|40334748|gb|CK368818.1|CK368818
EST:     GGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|60394469|gb|DN227339.1|DN227339
EST:     TCGGTACC-AG                         GAGG-ACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: TCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|60341353|gb|DN208326.1|DN208326
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|71446669|gb|DR827719.1|DR827719
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|211158395|gb|FK955819.1|FK955819
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|211235602|gb|FL469489.1|FL469489
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|211161585|gb|FK955846.1|FK955846
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|101401433|gb|EB822394.1|EB822394
EST:     CGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: CGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|60343233|gb|DN210206.1|DN210206
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|60340030|gb|DN207003.1|DN207003
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|211282256|gb|FL038858.1|FL038858
EST:     ATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: ATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|32802685|gb|CD954921.1|CD954921
EST:     GATCCTCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATACCAAGCGGATAGTCGGCTGC
genomic: GATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|24763662|gb|CA398833.1|CA398833
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|211282259|gb|FL038861.1|FL038861
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|32804663|gb|CD956899.1|CD956899
EST:     GATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|60353974|gb|DN220947.1|DN220947
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|32790022|gb|CD942258.1|CD942258
EST:     GATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|24768560|gb|CA403689.1|CA403689
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|5108358|gb|AI740071.1|AI740071
EST:     GGAAAAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|44901526|gb|CK828071.1|CK828071
EST:     GGAAGAAGCGGTTTGATATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGAGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|101401431|gb|EB822393.1|EB822393
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|60398986|gb|DN231802.1|DN231802
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
EST: gi|78026436|gb|DV494823.1|DV494823
EST:     GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC
genomic: GGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGC

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), 48 (downstream exon)
Score: 158

GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAGgttagttggc ... gttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgtgtactctgcataatgttattcatttcttcttttggtgctgttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG
                                           ctgttcct  CT-rich tract
               ataatgttattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagcttcagaagttttgggttaaagagtctgctacttttttttccttgtgtactctgcataatgttattcatttcttcttttggtgctgttcctgcagGAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - gcttcag
- - - - - - - - - - - - - - - ctgctac
- - - - - - - - - - - - - - - - - - - - - - -ccttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcata