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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG

Basic information

species Zea mays
transcript GRMZM2G081812_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
                   | |  || | |   |||| || |  || ||| || ||  |||  |||  | | |||||| |   | |    | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||                                              
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT

upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
                   | |  || | |   |||| || |  || ||| || ||  |||  |||  | | |||||| |   | |    | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG

upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
   ||  |       |     | || | |  |  |  | |||   |  |   | | |         |||  |||| | |   |  |  ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||
--gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttg-------gttggtaatattatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG

upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
   ||  |       |     | || | |  |  || | |||   |  ||  |   |  |||    |||  |||| | |   |  |  ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||                                              
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgttatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA

upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05390.2 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
   ||  |       |     | || | |  |  || | |||   |  ||  |   |  |||    |||  |||| | |   |  |  ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgttatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG

upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
---gtatgcttctaaccatca-tctata-tgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
      || |||| |     | || ||  |||||||| ||  |        | |  |||| | ||       || ||| | |    |  ||       |||| |||||||||||||  |||| ||    ||||| ||||||||||||||||||||||||
gtcagttgtttctgaatgcaactccatgctgtctttttgta-atgcagctgtggttatatgttat-------tttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG

upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcttctaaccatcat-ctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtct-tttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
||  | |  ||   | | | ||  |||| |  |      ||| || ||   |   | || || ||      | | | | |||| | |      | | |  |||||||||||||| |||| || |  ||||||||||||||||||||||||||||||
gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaac-----acactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG

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|113704302|gb|EE681806.1|EE681806
EST:     CAGCTTCGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|91053283|gb|EB163701.1|EB163701
EST:     CAGCTACGAATGAGGTATATTTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|78092548|gb|DV520922.1|DV520922
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29945732|gb|CB815791.1|CB815791
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|78103455|gb|DV521883.1|DV521883
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|32823254|gb|CD962976.1|CD962976
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|32809367|gb|CD961601.1|CD961601
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|78544622|gb|DV622120.1|DV622120
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|37375365|gb|CF624113.1|CF624113
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|78103456|gb|DV521884.1|DV521884
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|32823328|gb|CD963050.1|CD963050
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|22818962|gb|BU499052.1|BU499052
EST:     GGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: GGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|56382501|gb|CV985170.1|CV985170
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGCTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|78545018|gb|DV622516.1|DV622516
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|211367145|gb|FL432827.1|FL432827
EST:     TGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: TGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|32823027|gb|CD962736.1|CD962736
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|71305438|gb|DR788849.1|DR788849
EST:     AATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: AATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|21331386|gb|BQ486767.1|BQ486767
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC

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: 174

AGTTGGATCTTCACCTGCAGTATCCAATAATAAGGCGTCTGGTGCCCAACCAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

AGTTGGATCTTCACCTGCAGTATCCAATAATAAGGCGTCTGGTGCCCAACCAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 129

AGTTGGATCTTCACCTGCAGTATCCAATAATAAGGCGTCTGGTGCCCAACCAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 136

AGTTGGATCTTCACCTGCAGTATCCAATAATAAGGCGTCTGGTGCCCAACCAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
                    tgttaat  putative branch site (score: 136)
                                   ttttttgctgtctttt  putative PPT
      atatatgattgaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG