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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtcttaatgctctcaaatgcacattattaacttgaatgcgagattatgttttaaaattgatcctaatatttgtagatgtcatcagtatactgtgt...

Basic information

species Zea mays
transcript GRMZM2G126860_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtct---taatgctctcaaatgcacattattaacttgaatgcgagattatgttttaaaattgatcctaatatttgtagatgtcatcagtatactgtgt
||| ||||||||||||||||| || || |||||||| |||||||| ||||| |||||||| |||||||| || || ||||||||||||||||||||||||||||  | |   | ||  | | || |   | | || |  | |  ||| |  | |    || ||||   | ||   |  |||   | | |  |  ||| ||   
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggt-gcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga--

upper sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 3
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtcttaatgctctca-aatgcacat-tattaacttgaatgcgagattatgttttaaaattga-tcctaatatt-tgtagatgtcatcagtatactgtgt
 ||  |||||||||| |||||| |||| ||||||||||||||||| ||||| |||||||| || ||| | ||||| ||||| ||||| ||||| |||||||| |    || ||| |  ||   || | ||    | | | ||||   | | | |  || | | |||| |   |||||  || | | ||||  || |   || ||
ATTCGTTGATGAAATAGATTCTCTATGTGGTCAACGTGGAGAAGGGAATGAGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaataaatttatggtgccatggtgtagatacgctgattggaata--atactttagttgacatttgaattgcaatatcctgaacaagtca--agaagcttgagt

upper sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G39410.1 (Glycine max), 5'ss of exon 3
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtga-ggtcttaatgctct-caaatgcacattattaacttgaatgcg-agattatgttttaaaattgatcctaatatttgtagatgtcatcagtatactgtgt
 |||||||| |||||||||||  | || ||||| ||||||||||| || || |||||||| || ||  ||||||| || || ||||| ||||| |||||||| |  || |||||  | |     |  ||||| | || |  |||    ||  ||||      ||    ||  |       |  ||| |   |    | |||  
ATTTATTGACGAAATTGATTCCCTGTGTGGTCAGCGTGGAGAAGGCAACGAGAGTGAAGCTTCAAGACGGATTAAAACAGAGCTTCTGGTGCAGATGCAGgtaatagttttaatagtttgttggtttacatt-taaattgcaatatatagcatatgcgcggcaagctgtcaaatcccagttgtatggccatatatgaatgt--

upper sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G09300.1 (Glycine max), 5'ss of exon 3
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtcttaatgctctca-aatgcacattattaacttgaatgcgagattatgttttaaaattgatcctaatatttgtagatgtcatcagtatactgtgt
 ||  |||||||||| || ||| |||| ||||| ||||||||||| ||||| |||||||| || ||| | ||||| ||||| ||||| ||||| |||||||| | |  || ||| | |||   || |  |   | | ||| | | || ||| |  || | | ||||      |  |  |  |       || |   || ||
ATTCGTTGATGAAATAGACTCTCTATGTGGTCAGCGTGGAGAAGGGAATGAGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatttatggtgtcatggtgtagttacgttaattgga-gtgatattttagttgacatttgaattgcgttatcctgaacaagtcaagaagcttgagt

upper sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G30910.1 (Glycine max), 5'ss of exon 3
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtga-ggtcttaatgctct-caaatgcacattattaacttgaatgcg-agattatgttttaaaattgatcctaatatttgtagatgtcatcagtata-ctgtgt
 |||||||| |||||||||||  | || ||||| ||||||||||| ||||| |||||||| || ||  ||||||| || || ||||| ||||| |||||||| |  || |||||  | |   | |  ||||| | || |  |||    ||  ||||      || |  ||  || |    |   |  ||   ||||| |  |  
ATTTATTGACGAAATTGATTCCCTGTGTGGTCAGCGTGGAGAAGGCAATGAGAGTGAAGCTTCAAGACGGATTAAAACAGAGCTTCTGGTGCAGATGCAGgtaatagttttaatagtttgttagtttacatt-tgaattgcaatatatagcatatgcacatcaagttgtc--aagacgccttagtcccagttgtatagcccta-

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|18654969|gb|BM499774.1|BM499774
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|211363211|gb|FL271925.1|FL271925
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|32851188|gb|CD990869.1|CD990869
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTACTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|31353375|gb|CD437732.1|CD437732
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|32851418|gb|CD991099.1|CD991099
EST:     GCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTACTTGTTCTTGCTGCCACGAATACG
genomic: GCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|87152149|gb|DY396938.1|DY396938
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|211094373|gb|FL362897.1|FL362897
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|18654970|gb|BM499775.1|BM499775
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTC
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTC
EST: gi|22490133|gb|BU050056.1|BU050056
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|211363208|gb|FL271922.1|FL271922
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|37396249|gb|CF635412.1|CF635412
EST:     TGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: TGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|211363210|gb|FL271924.1|FL271924
EST:     AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG

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: 254

CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 566

CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 637

CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtctt ... tgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtcttaatgctctcaaatgcacattattaacttgaatgcgagattatgttttaaaattgatcctaatatttgtagatgtcatcagtatactgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT