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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttgttgagacgatggcgcattcagaatttcagactgcacagtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA

Basic information

species Zea mays
transcript GRMZM2G105631_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105631_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------------------------------------tttttttgttgagacgatggcgcattcagaatttcagactgcaca-gtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA
                                                                                                         | ||||| |||||   || |  |||| |    ||||   |||  | | ||||| |||    | || | | |  || ||| |   || |||        ||||| ||||| |||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||| |||||||||||||||||||| |||||||
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattga----ttcatgttgcctaagagagaaaaaaaatgagtttaacaagaat-tgcgt---cgtttt--------cagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA

upper sequence: GRMZM2G105631_T05 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
tttttttgttgagacgatggcgcattcagaatttcagactgcacagtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgca------gGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA
                   |  |||| | |||    | ||  |   || | |  |  | |  |  |   ||    | | |    ||||| |   || ||      ||||||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||| || || || || ||  ||||||| || ||| | |||||||
-------------------gtacattta-aataaatgtctttaagttggggaccatttcatttaaattgatagc-ttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
















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|9794218|gb|BE552526.1|BE552526
EST:     GGCCAGCCTC-AGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: GGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|211023209|gb|FK976627.1|FK976627
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|93284005|gb|EB676269.1|EB676269
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|71448756|gb|DR829806.1|DR829806
EST:     CTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: CTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|29167909|gb|CB411169.1|CB411169
EST:     GGGCTGGAAGTTCGTCTACCTCGG-GACGTCCAG                         GTG-AAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: GGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|33467925|gb|CF244974.1|CF244974
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|211023212|gb|FK976630.1|FK976630
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|71330488|gb|DR802010.1|DR802010
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|76018154|gb|DT945324.1|DT945324
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|76020765|gb|DT947935.1|DT947935
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|116829022|gb|EC863362.1|EC863362
EST:     TCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTA-CTTCAAGGCCTTCCGGGTTCCAGCAGCA
genomic: TCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCC-GGTTCCAGCAGCA
EST: gi|88757584|gb|DY541725.1|DY541725
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC

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: 167

GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 44

GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA
                                        atttgat  putative branch site (score: 96)
                                              ttcctgc  CT-rich tract
                                        atttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttgttgagacgatggcgcattcagaatttcagactgcacagtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA