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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaattgtgccgtcaagtagtgtccctgggctaaatgtaacatttatgtttatgccaatgtctattgcag

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 5'ss of exon 8
AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaa-ttgtgccgtcaagtagtgtccc-tgggctaaatgtaaca---tttatgtttatgccaatgtctattgcag
|||||| ||||||||||| |||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||   || ||||   |||  | | |||   ||   |  ||  |  | |||| |  |||||    | ||   |||||||  ||| ||  |    |     |  |  |  | || | | |   | ||| ||| || |||||| || |||||
AATATTTCTTGATGAAATTGATGCTATTATCAGCCAACGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGACGCTTGAAGACTGAGCTACTCATTCAGgtttctgcttgtttgaacatatcaaaattaagcttgctagtgtagcactccaagtcacggtttcctacttcataatctttc--agcttgaaactgtcccaactcccaacaaacaatacgtcagatttcaaagtttctatatttctgtcaatgtttactgcag

upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G26100.2 (Glycine max), 5'ss of exon 3
AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaattgtgccgtcaagtagtgtccctgggctaaatgtaacatttatgtttatgccaatgtctattgcag
|||||| ||||||||||| ||||| ||||| || || |||||||||||||||||||| |||||||| ||| | || ||||| |||||||| || ||||||||   |||||||||  | |  |   | | ||| |  ||       | |  | | |  | ||||  |    || || |  | ||  ||  ||    ||  |     | |                                                 
AATATTTCTTGATGAAATTGATGCAATCATTAGTCAACGTGGTGAAGCTCGCAGTGAACATGAAGCAAGTAGACGGTTGAAAACTGAGCTTCTCATTCAGgtgg-tgcttgtttc-ttacattttgaacaaactttttg-----taatcatca-agttaatttactacaccaagt-tcatactatctaaaacaaagcaatggtacactc------------------------------------------------

upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 8
AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaattgtgccgtcaagtagtgtccctgggctaaatgtaacatttatgtttatgccaatgtctattgcag
|||||| ||||| ||||| ||||| ||||| || || |||||||||||||||||||| || ||||||||| | || ||||| || ||||| || ||||||||   || ||||||  |       |  || ||  |  |        ||||||||       |||  |||   |  || | ||  | |   | | ||     |   ||      |   || |                                    
AATATTTCTTGACGAAATTGATGCAATCATTAGTCAACGTGGTGAAGCTCGCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtga-tggttgtttctt-------acaatgaacaaactt-------tttgtaat------cttcaagttaattaactgcaccaagttcatactatgtgaaaacaaagcaatggtacactga------------------------------------

upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 5'ss of exon 8
AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaattgtgccgtcaagtagtgtccctgggctaaatgtaacatttatgtttatgccaatgtctattgcag
 ||||| ||||||||||| |||||  | ||||| || ||||||||||  ||||||||||||||||| ||| | || ||||| || || |||||  | |||||      |  | |  |  |      | | | ||| ||     |  ||| |   | |  ||   |      || | |      |   || || |    |||||                                                      
TATATTTCTTGATGAAATTGATGCGCTTATCAGTCAACGTGGTGAAGGACGCAGTGAGCATGAAGCAAGTAGACGGTTGAAAACGGAACTACTCGTACAGgtgatctttaatcttttctttctcttttttatttattt---ttatttttatgtgatcacatcaatatcaatatatat------gaaatgcatggccttgtcaaactcaa------------------------------------------------

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|148995361|gb|EE034575.2|EE034575
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGC
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGC
EST: gi|60336952|gb|DN203925.1|DN203925
EST:     CAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: CAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|7216903|gb|AW563025.1|AW563025
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|7137663|gb|AW499208.1|AW499208
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|32837432|gb|CD977110.1|CD977110
EST:     GCAGTGAGCATGAGGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGT
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGT
EST: gi|32849820|gb|CD989501.1|CD989501
EST:     GCAGTGAGCATGAGGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGT
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGT
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|67012372|gb|CO441121.1|CO441121
EST:     GCAGTGAGCATGAGGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTNGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTA
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGA
EST: gi|9733829|gb|BE512581.1|BE512581
EST:     GCAGTAAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGCGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTAC
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATG-GTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTAC
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACA
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCT
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCT
EST: gi|32838514|gb|CD978192.1|CD978192
EST:     GCAGTGAGCATGAGGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAG                         ATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGT
genomic: GCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGT

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: 225

AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 205

AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 181

AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgctt ... tctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCGTGGTGAAGCTCGCAGTGAGCATGAAGCTAGTCGTCGCTTGAAGACTGAGCTACTTATTCAGgtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaattgtgccgtcaagtagtgtccctgggctaaatgtaacatttatgtttatgccaatgtctattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA