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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag

Basic information

species Zea mays
transcript GRMZM2G119169_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G37160.1 (Glycine max), 5'ss of exon 6
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatt--tggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag
|||||||||| || || |||||||| || || || ||||| |||||||||||||| ||||||||||||||| |  | |       | |||||  ||    ||   ||  ||     | |  |  | |  || || | ||||| | ||   | ||           
CTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAGgtaatgattgaccatctctctgttaacagtatatatacttcctcttttcttttgcatcaaattcttat-ctattattgtt-cttgtag---------

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G01110.1 (Glycine max), 5'ss of exon 6
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatt--tggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag
|||||||||| || || |||||||| || || || || || |||||||||||||| |||||||| |||||| |  | |       | ||| |  ||    |||  ||  ||     | |  |  | |  || || | ||||||| | |  | ||           
CTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAGgtaatgattgaccatctctctgataacattatattgacttcctcttttcttttgcatcaaattcttat-ctattgttg-ctcttgtag---------

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctg-----actgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag
||||||||||   ||| |||||||| ||  | || ||||||||||| |||||||| ||||||||||||||| ||   |     ||  |  |    |||| |||||      ||| | |        | |    || | |   ||  |  |  || | ||| |   |||
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctct--ctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag
|||||||||||  ||| |||||||| ||  | || |||||||||||||||||||| || || ||||||||| |   | ||  |     || | |    | |    ||||  |    |   |  ||   |||| |  | | ||  |  ||  |         ||
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaa---aaattcaggact--agtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
lower sequence: PP1S38_376V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgta--tttggttttgtacactgtttgcacctgatt-atctgactgaaagcgtgggatt--aatgttgttgtgctattgtggtcattcgtttcctcgtcag-----------------------------------------------
||||||||||||| || |||||||| || || ||| | || |||||||||| ||| |||||||||||||||  ||| | |    |    | | |||   | || |  |   |    |    |  ||   || |||||  |  | |||       |  ||    || |                                                
CTTACATGTCCTCTCCTTGCCACATTGAGCTGATCCTTTCTGAGAAGGAAGCGCCAGTGAAGAAAGAGgtaattttagatgctaaattagatggcaaaagttttagatagtttcctgtcctgtttttcgattttgtttcgtgactgtaaattcacaatttacagttatttataattcagaactgtaaattaaccggttctttacgggctttgcag

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|60396530|gb|DN229399.1|DN229399
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|67011457|gb|CO440206.1|CO440206
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|30704734|gb|CD058588.1|CD058588
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|4885932|gb|AI677052.1|AI677052
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|9952004|gb|BE638587.1|BE638587
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|101386822|gb|EB815428.1|EB815428
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32848019|gb|CD987700.1|CD987700
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32934714|gb|CF039526.1|CF039526
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|37390893|gb|CF632684.1|CF632684
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|113801487|gb|DW924047.1|DW924047
EST:     AGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: AGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|211372347|gb|FL430779.1|FL430779
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|13178113|gb|BG349371.1|BG349371
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|33097211|gb|CF057171.1|CF057171
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|5525695|gb|AI861588.1|AI861588
EST:     GCCCCATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32837215|gb|CD976893.1|CD976893
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|14701011|gb|BI233429.1|BI233429
EST:     CCACATC-AAGCTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: CCACATCGAA-CTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag

- - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA