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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccgatgtgtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgacctttgtcatctgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG

Basic information

species Zea mays
transcript GRMZM2G157836_T07
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157836_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 3'ss of exon 1
tccgatgtgtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgaccttt-gtcatctgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG
                || | |||| |  |           || |   || |||     |||   ||    ||   |||| ||| || | || | | ||||||||||| ||||| || ||||| |||||||| || || || |||||||| |||||||| ||| ||||| |||| ||||||||||||||||| |
-------------gttaagctcagc-tgctcacacatggcgcgttatcgt-agcctcagcgtagtggagactctagtgactttttgttagctatgtcgcagGCCAGCGTAAGCTCTCGCAGTCATCGATTTTGGTGGTGGGCGCTGGAGGATTGGGCTCGCCCGTGGCACTGTACCTAGCAGCTTGTGGTGTTG

upper sequence: GRMZM2G157836_T05 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G02260.1 (Glycine max), 3'ss of exon 1
tccgatgt-gtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgacctttgtcatctgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG
    |  | | ||||| |     |||   ||    |       |      ||       | || |    |  |||      |||     | ||    ||||| |||   || || |   ||||||| || |||||||| |||||||||||||||||  | ||       || ||  | ||||||| |||||| |
cgaaaaatagacatcagacaaatagccc-ttatctgcatgtttgtcttgttttttttttttgtcttaaattttcccaccttcttgtgtttgtggagtgcagGGCAGGCAAATCTATTGAAGTCGTCAATCTTAGTTGTGGGAGCTGGAGGTTTGGGTGCACCTGCATTGTTATACTTTGCAGCTTCTGGTGTTG

upper sequence: GRMZM2G157836_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0090g01020.t01 (Vitis vinifera), 3'ss of exon 1
tccgatgtgtcatcacaatcgcagcatattgctggg-gaaaacggtgcagttagcacgct-cgtttcggctgatcctctgacctttgtcatctgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG
  | ||   | |||    |      ||||   | |  |  |   ||  | |  |   | |   | |   ||   |   ||   |||||  |  |    | ||| |||  ||  || |   |||| || ||||||||||||||||||||||| |||||| | ||       || ||||| || || ||||| || |
agcaatcaataatctactttattctatataattagttgtcatttgtttattctgattggtatctctttactttccaattggtatttgtggttggct--gtagGGCAGTCGAGTCTCTTGAAGTCTTCAATTTTAGTTGTTGGAGCTGGAGGATTGGGCGCACCAGCTCTTTTATATCTTGCGGCATGTGGAGTTG

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|91051873|gb|EB162291.1|EB162291
EST:     CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGG                         GGCAGCGGAAGCT
genomic: CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCT
EST: gi|78087902|gb|DV516295.1|DV516295
EST:     CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTT
genomic: CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTT
EST: gi|101400847|gb|EB822121.1|EB822121
EST:     CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTT
genomic: CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTT
EST: gi|50332338|gb|CO527464.1|CO527464
EST:     GTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCCAGG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGT
genomic: GTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCC-AGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGT
EST: gi|71445496|gb|DR826546.1|DR826546
EST:     CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTT
genomic: CGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTT

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 3 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 18

AAGAAGGGATCAAGGAACAGCGACCAGAGAAAGGCTGCGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG


Block sizes: 34 (upstream exon), 39 (downstream exon)
Score: 4

AAGAAGGGATCAAGGAACAGCGACCAGAGAAAGGCTGCGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 12

AAGAAGGGATCAAGGAACAGCGACCAGAGAAAGGCTGCGTCTGCTGCTGCTCCTACGGCTGCTGATGCTACGAACAAGAGGCCCAGGgttagtgcct ... tgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagttagcacgctcgtttcggctgatcctctgacctttgtcatctgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG
                            ctctgac  putative branch site (score: 12)
                                           tctgtct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccgatgtgtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgacctttgtcatctgtctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGAGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT