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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctcatttctagtgctatgtaattgctgccaacatttaccatataatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG

Basic information

species Zea mays
transcript GRMZM2G130440_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 5
ttgctcatttctagtgctatgtaattgctgccaacatttaccatataatca------tgtaatc-ttaatagccatgaatacctcaataatctcccat--gtcatgt---agGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
| | ||||||| ||||| | || |||| || || ||| ||||||| |||| ||| | ||||| ||||| || ||| | ||||| | |||||||||||| ||||| |||||||| |||||||| ||||| |||||
---------ttgaatgctatgg---tgctggcgacctttatcacatgctcaaattcttgtaatccttaacagcgactaatacatcaattatttcctttttgtcatattttagGTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG

upper sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 5
ttgctcatttc-tagtgctatgtaattgctgccaacatttaccatataatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
||| || | | | | | | || || | | | | || | | || || | | || || | | || || ||| | ||| |||||||||||||||||||| |||||||| || ||||| || ||
ctgcattttgcatcatacagtccactttctatgatctgattttttttatgtgttgtttttttattgtaactaaaacat-gttcatttctgttgtgcttcagGATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG

upper sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 6
ttgctcatttctagtgctatgtaattgctgccaacatttaccatataatcatgtaatcttaatagccatgaatacctcaa--taatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
| || | ||| | | | | | | | | |||| | |||| || || || | || || | || || ||| ||| |||||||||||||||||||| |||||||| || ||||| || ||
-catctagtttgactgcattttgcatcatacagtcctactttaaataacgttttaatgttttta-ttataactaaaacatgttcatttctgttgtgcctcagGATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG

upper sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 7
ttgctcatttctagtgctatgtaattgctgc--caacatttaccatataatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
|| || | | | ||| || | ||| | | | | | | || | || | | | | | | | || || ||||||||||||||| |||||| | ||||||||||| ||||| |||||
--gccatgttgagaagttttataactgataatgcaatgtggaaatttttgtgtttctgctttcttttcccagcgttaatggaaattttttgtggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG

upper sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ31432 (Selaginella moellendorffii), 3'ss of exon 6
ttgctcatttctagtgctatgtaattgctgccaacatttaccatataatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgt-agGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
|| || | | | || | | || | | | | | | | | | ||||||||||||||||||||| ||||||||||| || || || || ||
------------------------------------------gtacgatgaatgagttttcttctttgttaaacttttatttgttgtgcctttgttctcagGTTGGAATGCTTGCATTGCCTTGGTCTGTGGCAACTGCGTTGTATG

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|211391225|gb|FK985220.1|FK985220
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAAATGTG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTG
EST: gi|211380677|gb|FK985162.1|FK985162
EST:     GGAGNNTGTGG-TGTTATA-CGGCATTTAATTTCCCT-GTGCTGTGCTTG                         GNTGGAATGCT-GCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
genomic: GGAGT-TGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|211380667|gb|FK985152.1|FK985152
EST:     TGGAGCTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGTAATTGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|211393851|gb|FK985233.1|FK985233
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGC
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGC
EST: gi|211267399|gb|FK985118.1|FK985118
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTACTTTCCCTTGTGCTGTGCTTG                         GCTGGAATGCTGGCATCGCTTTG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTG
EST: gi|211380674|gb|FK985159.1|FK985159
EST:     GGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGNAATTTGTGTCGTCTGG
genomic: GG-AGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATT-GTGTCGTCTGG
EST: gi|149072859|gb|EE161112.2|EE161112
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GGTGGAATGCTTGCATTGCTTTGGTCTGGGGAA-TTGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|211383313|gb|FK985176.1|FK985176
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGGATGCTTGCATTGCTCTGGTCTGTGGAAAATGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|78180622|gb|DV550950.1|DV550950
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
EST: gi|7844452|gb|AW787674.1|AW787674
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
EST: gi|211519446|gb|FK985264.1|FK985264
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|211269838|gb|FK985131.1|FK985131
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAAATGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|211267389|gb|FK985108.1|FK985108
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|7844027|gb|AW787230.1|AW787230
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
EST: gi|211396477|gb|FK985252.1|FK985252
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGG
EST: gi|7844028|gb|AW787231.1|AW787231
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
EST: gi|211519438|gb|FK985256.1|FK985256
EST:     TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG                         GTTGGAATGCTTGCATTGCT
genomic: TGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCT

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: 291

GTGTGGAATCCCCTTGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 494

GTGTGGAATCCCCTTGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GTGTGGAATCCCCTTGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

GTGTGGAATCCCCTTGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtctct ... tgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
           tcttaat  putative branch site (score: 302)
 tctcccat  putative PPT
 atgtaatcttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctcatttctagtgctatgtaattgctgccaacatttaccatataatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG

-tgctcat
- - - - - - - tgctatg
- - - - - - - - - - - - ttgctgc
- - - - - - - - - - - - - - - - - - - - - - - - -catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgaa