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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcggttgaacactcaaagatttactcatccaacatgttgttctgtggttgtctgtattcttagttatgctaagatgcatgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC

Basic information

species Zea mays
transcript GRMZM5G836588_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 3'ss of exon 3
tagcggttgaacactcaaagatttactcat--ccaacatgttgttctgtggttgtctgtattcttagttatgctaagatgcatgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
 | | |    | | | ||| | ||  | ||  |  |  |  ||||     || || ||  ||||| ||||  ||||  |   | | |||||| ||||| |||||||||||| ||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || || || |||||||| |||
aatctgacatata-tgaaaaagttgttgattactgatttactgtttcacagtggtgtgatttctttgttacactaaattttttatctcaatttattat-cagGAAGGTCATTCATACAGTCGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTACCGTTCTTGTTTGGAACTCCTC

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 4
-tagcggttgaacactcaaagatttactcatccaacatgttgttctgtggttgtctgtattcttagttatgctaagatgcatgtatcaattga---ttatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
 || |    | |  ||    || ||    ||  |   ||   |    | || | ||   | |  |  |     || |||  | | |   |||    || | ||||| ||| |||||||| || || ||||| ||||| || |||||||| |||||||| |||||||| || |||||||||||| | || ||  ||||||| |||
ataccaa--gcattctgtgcgactttaatatggactgtgaaatagatttgt-gccttagtccccaact-caaaaaaatgtgttttttgtttgtcttttgttcagGAGGGTTATCCATACAGTAGGACCCAAGTATGCAGTAAAGTATCATACAGCTGCTGAGAATGCTCTAAGTCACTGCTATAGATCTTGTCTGGAACTTCTC

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
tagcggttgaacactcaaagatttactcatccaacatgtt-gttctgtggttgtctgtattcttagttatgctaa--gatgcatgtatcaattgattat---gcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
         | ||   ||     |||  |  | |  ||||   | |  ||   | ||| |  |   | | ||| |  ||| | ||| ||     ||  |   | |||| ||| || ||||| ||||| ||||| ||||| || || ||||| || ||||||||||||||  | ||||||||||||||||| ||| | ||||| || 
------catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S37_110V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------tagcg-gttgaacactcaaagatttactcatccaacatgttgttctgtggttgtct-gtattcttagttat---gctaagatgca----------tgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
                                                         |||   ||  | ||||  | |   ||  ||||    ||  |  | | |  ||||   | ||||| | | |    | ||  ||  |          ||  |   |||||| ||||||   || || ||||| ||||| || | |||||| |    ||| |||||||| || ||||||||| | |||||||||||||| || ||| ||||||| || 
gtatgttattggttaaggatttctgccgattttttcagcagcattgtttgcctactctagtaagtccatcact--aggtagtatccatcggcaatccttctgtatacttgttcagaattctaaatcagatggttacaatttacagtaggggttggcttggttgatt-tgcagGCGTGTGATTCATACAGTGGGACCTAGATATGCAGCACGGTACCACACAGCAGCTGAGAATGCATTGAGTCACTGCTATCGTTCATGCCTGGAACTTCTT

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ24833 (Selaginella moellendorffii), 3'ss of exon 3
tagcggttgaacactcaaagatttactcatccaacatgttgttctgtggttgtctgtattcttagttatgctaagatgcatgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
                                             ||  |||    |    | | ||     | |||    |||     |  || |  |||   ||||| || || ||||| ||   ||| ||||| ||||||||||||||||| || ||||| || ||||| |||||| |||| ||  | || || || 
---------------------------------------------gtacttggaaatcacatcattttgtgcatgatcatagtac--gctttttctctagGCGTGTCATTCACACTGTGGGTCCTCGATACGCTGTGAAGTATCACACAGCTGCTGAAAATGCCCTGAGTCATTGCTATAGGTCTTGTCTTGAGCTCCTA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ30302 (Selaginella moellendorffii), 3'ss of exon 3
tagcggttgaacactcaaagatttactcatccaacatgttgttctgtggttgtctgtattcttagttatgctaagatgcatgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
                                             ||  |||    |    | | ||     | |||    |||     |  || |  |||   ||||| || || ||||| ||   ||| ||||| ||||||||||||||||| || ||||| |||||||| |||||| |||| ||  | || || || 
---------------------------------------------gtacttggaaatcacatcattttgtgcatgatcatagtac--gctttttctctagGCGTGTCATTCACACTGTGGGTCCTCGATACGCTGTGAAGTATCACACAGCTGCTGAAAATGCCCTTAGTCATTGCTATAGGTCTTGTCTTGAGCTCCTA

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|211381535|gb|FL250722.1|FL250722
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
EST: gi|76286118|gb|DV025686.1|DV025686
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
EST: gi|93016568|gb|EB642088.1|EB642088
EST:     CCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
genomic: CCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
EST: gi|211381540|gb|FL250727.1|FL250727
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTNCA-GTATCACACAG
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGT-CAAGTATCACACAG
EST: gi|211378900|gb|FL250717.1|FL250717
EST:     TGCCGAACTGGGATGGCCAAGATGACCCATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCC
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCC
EST: gi|91051901|gb|EB162319.1|EB162319
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
EST: gi|211381541|gb|FL250728.1|FL250728
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCA-G                         GNAAGGTCATNCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAG
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagG-AAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAG
EST: gi|148931777|gb|EC875053.2|EC875053
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
EST: gi|94478487|gb|EB707445.1|EB707445
EST:     TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG                         GAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC
genomic: TGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGC

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: 48 (upstream exon), 46 (downstream exon)
Score: 47

GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 57

GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAGgtaagctggg ... gattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggttgtctgtattcttagttatgctaagatgcatgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC
                                         aattgat  putative branch site (score: 64)
                                     tatcaattgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcggttgaacactcaaagatttactcatccaacatgttgttctgtggttgtctgtattcttagttatgctaagatgcatgtatcaattgattatgcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- gcggttg
- - - - - - actcaaa
- - - - - - - - - - - - - -catccaa
- - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt