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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtgaatcctacataagtacttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtggtcaacacgctattgattgtttcag

Basic information

species Zea mays
transcript GRMZM2G146677_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146677_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 5'ss of exon 7
AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtgaatcctacataagtacttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtggtcaaca-cgctattga-ttgtttcag
||| ||||||||||||||||||||||||||||||||||||||||| || |||||||| | |||||||||||| |||||||| ||||| ||||| ||||||||||     |||  ||   ||| ||| ||| |||| ||          | | | |||||||     |||||  | | ||    ||  | || | ||| | ||  |||| ||||
AAGGCCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTCTCCATAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaa-----gaagtct---taactacgtaa-gttccta---------atagattaatctat-----gtgaagcatggaaaggagt--ttaatatcgccactgggttgtctcag

upper sequence: GRMZM2G146677_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA06G42830.1 (Glycine max), 5'ss of exon 7
AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtgaatcctacataagtacttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtggtcaacacgc-tattgattgtttcag--
 ||||| |||||||| ||||||||| | ||||| |||||  | |||||||   ||||  |||||||||| |||||||  || ||| | |||||||||||||||||  |         ||| | | ||||  || |     |  ||       |   |   || | | || | ||  |  || | || ||| |||    | | |  |   ||   
TAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTTATAGTTTCTACTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgc--------cattatttcttagagtcccctcctccct------ctccctgggttttcaatgtagaagtagtgattttgatcatcacatacaataaacgaaccaaac

upper sequence: GRMZM2G146677_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT2G30970.1 (Arabidopsis thaliana), 5'ss of exon 7
AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaa--tcgtgaa----tcctacataagt-acttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtgg--tcaacacgctattgattgtttcag------
 |||||||||||||||||||||||| | |||||||| | | | || || |  || ||    || ||||| || |||||| ||||| |||||||||| |||||||   |  ||||    | |||  |   | | | |||   |||||||  | | ||       | |||  ||||| |  ||  |  ||||         | | || ||   |    || |      
TAGACCAATGTACAGCAACCCACCTTTGCATGGTGCTCAGCTGGTCTCAACCATTCTTGAAGACCCAGAGTTAAAGAGTCTGTGGCTAAAAGAAGTTAAGgtaacatttatgaaaaaatgctaattctttcattcaattaccttatatc-ccatgttcactcttttatgtttagtaatcaactatggaattaaaatctgataagccatatgtaaaatctgtaacag

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|31349057|gb|CD433414.1|CD433414
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|6056460|gb|AW090850.1|AW090850
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|31362346|gb|CD446703.1|CD446703
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|32908144|gb|CF012957.1|CF012957
EST:     TAATCCTCAGTGACCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAGTCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|32833423|gb|CD973101.1|CD973101
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|31353746|gb|CD438103.1|CD438103
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|211235538|gb|FL127822.1|FL127822
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|5714296|gb|AI944281.1|AI944281
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|5847048|gb|AW000127.1|AW000127
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|31352769|gb|CD437126.1|CD437126
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|84977385|gb|DW475807.1|DW475807
EST:     TAATCCTCAGTGATCCAGAATCGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|50324321|gb|CO519447.1|CO519447
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|5846903|gb|AI999986.1|AI999986
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|18172785|gb|BM348173.1|BM348173
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|211237763|gb|FL127823.1|FL127823
EST:     AATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: AATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTT-AAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|211237764|gb|FL127824.1|FL127824
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|5296287|gb|AI783057.1|AI783057
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
EST: gi|32834200|gb|CD973878.1|CD973878
EST:     TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT
genomic: TAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 62

AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 166

AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtg ... attgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtgaatcctacataagtacttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtggtcaacacgctattgattgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT