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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatctatcattttttcctagcctttccttccttatactatatcttatatatctggatattaaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG

Basic information

species Zea mays
transcript GRMZM5G816609_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 20
gttcgtatctatcatttttt-------------cctagcctttccttccttatactatatctta-----tatatctggatattaaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG
||| ||||  || | |||||             || |   | |  |  | ||    ||  ||||     |||| ||| ||  |||||||||| |||||||||| || ||||||||||| ||||||||||| ||||||||||| ||||||||||  ||||||||||||||||||||||| || ||||||||||| |
gtttgtattcataactttttaacccacgacatacccaatatattttgtcctaattgatggcttacgttttatacctgaat--taaatttctctagGCTGCAATCATTTCATTGGGTTTCATTGGTGCTGGTACAAACAATGCTAGAATAGCTGGTATGCTTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTG

upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 20
gttcgtatctatcattttttcctagcctttccttccttatactatatcttatatatctggatattaaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG
||  |    ||   | ||||| | |    |       ||||   ||| || ||  |      |||||  | || ||||| ||| |||| || |||||| | || |||||||| || ||||||||  |||| |||| ||||||||||||||||||||||||||||||||| ||  |  
gtaagatgttagtctcttttctttgaacatttgggtctatatcttat-ttgtagctaaaacaattaatatgcttcagGCGGCAGTTATATCCTTGGGTCTAATAGGTGCTGGAACGAACAATGCTCGAATTGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAGGATACCA

upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 20
gttcgtatctatcattttttcctagcctttccttccttatactatatcttatatatctggatattaaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG
||  |    ||   | ||| | | |    |       |||| | ||| || ||  |      ||| |  | || ||||| ||  ||||||| |||||| |||| |||||||| || ||||||||  |||| |||| |||||||||||||||||| |||||||||||||| ||  |  
gtaagatgttagtctctttactttgaacatttgggtctatattttat-ttgtagctaaaacaatttatatgcttcagGCAGCTGTTATCTCCTTGGGTCTGATAGGTGCTGGAACGAACAATGCTCGAATTGCTGGCATGCTTCGCAATCTTTCTAGTTATTACTACAAGGATACCA

upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 20
----------gttcgtatctatcattttttcctagcctttccttccttatactatatcttatatatctggatatt---aaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG
               || |  |  | || ||  ||   |||  ||  |||| |    | || |       |||||       |||| ||||||||  | ||||| ||||||||||| ||||| || || ||||||||  |||| |||| |||||| || ||||||||||| |||||||||||||||||  
gtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattg--gcctaaacgcagaaatatttgtgggattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTA

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|67025197|gb|CO453946.1|CO453946
EST:     TGGACACACTGAGTAGATTTAGTCCTGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGTGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|87157733|gb|DY402522.1|DY402522
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|31361134|gb|CD445491.1|CD445491
EST:     ATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: ATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|32911849|gb|CF016661.1|CF016661
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|89763994|gb|DY690961.1|DY690961
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|26559722|gb|CA831957.1|CA831957
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|67013648|gb|CO442397.1|CO442397
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|67041940|gb|CO468195.1|CO468195
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|71764383|gb|DR962320.1|DR962320
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
EST: gi|22819353|gb|BU499443.1|BU499443
EST:     TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATG                         GCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA
genomic: TGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGA

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), 49 (downstream exon)
Score: 149

GTGAATGTTATGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG


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

GTGAATGTTATGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

GTGAATGTTATGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GTGAATGTTATGGACACACTGAGTAGATTGAGTCATGATGCCGATGCCGATGTGTCAATGgttcgtatct ... atttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcctttccttccttatactatatcttatatatctggatattaaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG
                                              tttctcc  CT-rich tract
              ttatactatatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtatctatcattttttcctagcctttccttccttatactatatcttatatatctggatattaaatttctccagGCTGCAATTATCTCATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC