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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcag

Basic information

species Zea mays
transcript GRMZM2G047564_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g39344.3 (Oryza sativa), 5'ss of exon 6
AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtaccc-gctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcag
||| |||| ||||||||||||||||| ||  ||||||| |||||||| |||||||||||||||||||| ||||| ||||| | ||||| ||||||||||||||| | ||| | || |         ||  ||  |  |  ||   |  | ||||    |    ||| ||   ||      |    | |  || |      ||  |||     |||| | |  | || || ||                 | || |||   || |  || |  || || ||||||
AAGTTTTTACCATATATCATTTCTTCCTTTGGTCCTGACAAATCAGTTGCTGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgcttttaagc---------taaggcgtcaagagaatgttgttatatt---tatgcacaagtgccaac------agtgtttctatattgagaccgttttata----aattcagtttagtactgact-----------------agttgcacgtgtatccttttcattgttgtctgcag
















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|76012489|gb|DT939659.1|DT939659
EST:     CTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: CTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|71312657|gb|DR792849.1|DR792849
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|60398946|gb|DN231762.1|DN231762
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|18166670|gb|BM336509.1|BM336509
EST:     GCTAAAGAAATGTAGCCGAAGTGGTGATGCTCCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: GCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|78083152|gb|DV511545.1|DV511545
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|88750160|gb|DY534301.1|DY534301
EST:     TGAATTTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|60346890|gb|DN213863.1|DN213863
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|60345004|gb|DN211977.1|DN211977
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|76280673|gb|DV020241.1|DV020241
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|37379970|gb|CF626760.1|CF626760
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|149097994|gb|EE183939.2|EE183939
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|211171388|gb|FL176740.1|FL176740
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|76012490|gb|DT939660.1|DT939660
EST:     GTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: GTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|18165516|gb|BM335355.1|BM335355
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|60399515|gb|DN232327.1|DN232327
EST:     AATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: AATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|91873503|gb|EB403460.1|EB403460
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|211528664|gb|FL445658.1|FL445658
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCATTGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|88749306|gb|DY533447.1|DY533447
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT

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 3 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 22 (downstream exon)
Score: 2

AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 2

AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA


Block sizes: 42 (upstream exon), 24 (downstream exon)
Score: 4

AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG