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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttataacattttaattaaaagcaactgtttgcaattttgcatactgaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
---------------------------------------------------ttataacattttaattaaaagcaactgtttgcaattttgcatactgaagatcaaacttttcat-actgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
                                                     ||||   || |   || ||| | | | |    |  || ||  |||      ||||    || | || | |||  |   | ||  | | ||| |||| |||||||||||||||||| || |||||||||||||| || || || ||||| || |||||||| |||||||  || || |||||||||||||||||||| ||
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcat---tattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 21
-------------------------------------------------------------------------ttataacattttaattaa--aagcaactgtttgca-attttgcatactgaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
                                                                         |||| |  || |||  ||  ||   | || || ||   |  ||  | | | | ||| |      ||       || |   | |  || || |  | | |  |||||||||  || |||| || || ||||| |  || |||||||| |||| ||| ||||||||||||||||| ||||||||||| ||| |||||||||| ||
gtatattttgtaaccttttctcttactgtttgtattccctactgatgacctatttaatgtgtagctgactttgttattaacttgtaaccaagtaatggattgcttacatgctgagctgagtaatggtcagatacaaaatctgttttgactaaatatgatg-tcctcatcctatcagATTATGACCGAGTTATTAAGAACATTGAGAAAGGAGAAGCAAGGATATACCGGAAGGATGAGATTATGAAAGCTATTGGGAAAAAGCTAGACCGCTATAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
--ttataacattttaatt----aaaagcaact-gtttgcaattttgcatactgaagatcaaacttttcatactgacagattt-tgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
  ||      | || |||    ||| | | || |  |  | |||| |||     | |||||   |      ||| | ||||| |||  ||||||   || |   | |||||||||||||||||| ||||| |||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||||||||| |||||||||||
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccat-taagatatcaagggt------ctgtctgatttgtgtactttgatttatggtttgc-agATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
ttataacattttaattaaaagcaactgtttgcaattttgcatactga---agatcaaacttttcata--ctgacagattt-tgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
   ||| || | ||           ||| ||    |||||  | ||      || ||| | |  |    ||| | ||||| |||  |||| |   || |    ||||||||||||||||||| ||||| |||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||||||||| |||||||||| 
--ttaaaatatcaa---gggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttg-tagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
ttataacattttaat----taaaagcaactgtttgcaattttgcatactgaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
  ||||   |||  |    |||      |||      | |||   |   |||  |   |   |||   || |  | |    | |||| ||||||||      ||||||||| |||||||| ||||| |||||||||||||| |||||||| || || || |||||||| |||||||||||||| |||||||| |||||||||||
-gataaggctttgttgctttaattttttctggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgc-attttttaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 21
------ttataacattttaattaaaagcaactgtttgcaattttgcatactgaagatcaaacttttcatactgacagattt-tgtgttttga-tcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
       ||   | || | |||||       ||      | |||   |   |||  ||||  ||      ||| |  |||| ||  |||||| |||||||      ||||||||| |||||||| ||||| |||||||||||||| |||||||| || || || |||||||| ||||| |||||||| |||||||| |||||||||||
agtgggataaggctttgttattaactttttttggaaattactttctgtttagaatgtcaaggtt------ctgcctaatttgtgcattttgaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAAGCTATTGGAAAGAAGTTGGACCGCTACAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
-ttataacattttaattaaaagcaactgtttgcaatt--ttgca-tactgaagatcaaacttttcatactga-cagattttgtgttttgat---cattgttcaact---agATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
 |||  |  |||  |||   |   |  |||    | |  ||||| | |   | |      | || || || |  |   | ||  | ||| |   | ||||  || |   |||||| || ||||| || || |||||||| || |||||||||||||| ||  | || ||||| || ||||| ||||||||||||||  | || ||||||| 
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
--ttataacatt-ttaattaaaagcaactgtttgcaattttgcatactgaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
  ||   | ||| | |  |  |    ||    | || || |   |  | || ||     ||||      | | | ||||     || |  |   ||   | |||||||||||| || || || || |||||||| || || || ||||| ||  | || |||||||| ||||| || |||||||||||||| || ||||||||
ggttgatatattgtcagatgcatcttacaacatccatttgtttttcatcaaaatggtgattttt---tcgtctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA

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|166697114|gb|EG203494.1|EG203494
EST:     GTTCAACGCTTATGCTAAAGTTTTCAAGGAGAGATACAAGGAGCTGAGTG                         ATTATGATAGAATTATAAAAAA
genomic: GTTCAACGCT-ATGCTAAAGTTTTCAAGGAGAGATACAAGGAGCTGACTGgtacggcagt ... gttcaactagATTATGATAGAATTATAAAAAA




















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: 503

AATGATATTAAAAGTATATCCTCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGCTATGCTAAAGTTTTCAAGGAGAGATACAAGGAGCTGACTGgtacggcagt ... gttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

AATGATATTAAAAGTATATCCTCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGCTATGCTAAAGTTTTCAAGGAGAGATACAAGGAGCTGACTGgtacggcagt ... gttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

AATGATATTAAAAGTATATCCTCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGCTATGCTAAAGTTTTCAAGGAGAGATACAAGGAGCTGACTGgtacggcagt ... gttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

AATGATATTAAAAGTATATCCTCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGCTATGCTAAAGTTTTCAAGGAGAGATACAAGGAGCTGACTGgtacggcagt ... gttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
       aaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttataacattttaattaaaagcaactgtttgcaattttgcatactgaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - aagcaac
- - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt