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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcttttctttcttccctagctttctcttctttgcctgtggggcgtatttacacctgtccaccgataaatctgattgagattgtattgggaagttgaatttatcactaacacaagtttcagtttattttgagtaatttaaatgtttgtttcaatgttgtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT

Basic information

species Zea mays
transcript GRMZM5G806449_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 8
gttatcttttctttcttccctagctttctcttctttgcctgtggggcgtatttacacctgtccaccgataaatctgattgagattgtattgggaagttgaat--ttatcactaacacaagtttcagttt---attttgagtaatttaaatgtttgtttcaatgttgtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT
                                                                              |||||   | || || | || | |    || |       | | |    |||   | |   ||||||||   |  ||  ||||||||| | | |||||||||| || ||||||||||| || |  || | | |||||||||||||||||||||| |||||||| |||||||||||||||||| |||||||||| || |
---------------------------------------------------------------------------atgtgagaccatcttaggcatttaattggccattatctttgtatgatattctttgagactacaagtaatttgtgttgtttattcaatgttctatttttagGTTGATGATTATTCTCGTACATCAGTCCCAAATATATGGGCTGTGGGTGATGTAACGAACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCT

upper sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 11
gttatcttttctttcttccctagctttctcttctttgcctgtggggcgtatttacacctgtccaccgataaatctgattgagattgtattgggaagttgaatttatcactaacacaagtttcagt---ttattttgagtaatttaaatgtttgtttcaatgttgtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT
                                                                          || ||  |    |    |||  |||| || | || |     |||    ||    | ||| ||| | | ||  |  | |  | | ||  | | | ||||||| || || ||||| || ||       |||||  ||||||||||||||||||| |||||||| || ||| |||| || || || |||||||| ||| | |
-------------------------------------------------------------------------atgctttcgtcaatgactggatattgatttgaacaattgtttaagagctagagaatgattatgactcagttctaaatgttctgcgatcctttgtgtttagGTGGATGAGTATTCCCGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTAACTCCGGTGGCCTTGATGGAAGCATCGT
















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|161407234|gb|DW042290.1|DW042290
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGA-TATTC
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTC
EST: gi|211287654|gb|FL367858.1|FL367858
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|76293304|gb|DV032872.1|DV032872
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|211368053|gb|FL471715.1|FL471715
EST:     CGTTGAGATTGA-CGGG-TGGAGCCCATCAAG                         GTTGACGAATATCCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGA
genomic: CGTTGAGATTGACCGGGTTGGAG-CCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGA
EST: gi|62550294|gb|DN830714.1|DN830714
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|67018787|gb|CO447536.1|CO447536
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|8368856|gb|BE051801.1|BE051801
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|211462691|gb|FL336836.1|FL336836
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|211123447|gb|FL321141.1|FL321141
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|67026810|gb|CO455559.1|CO455559
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|76012766|gb|DT939936.1|DT939936
EST:     TGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|211135367|gb|FL349825.1|FL349825
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|32919439|gb|CF024251.1|CF024251
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|32794339|gb|CD946575.1|CD946575
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|91056621|gb|EB167039.1|EB167039
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|24934507|gb|CA452725.1|CA452725
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGT
EST: gi|211396212|gb|FL320934.1|FL320934
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|47961736|gb|CN844445.1|CN844445
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|211460047|gb|FL333663.1|FL333663
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|51593048|gb|CV072194.1|CV072194
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|47962782|gb|CN845491.1|CN845491
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCCGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|33942527|gb|CF349127.1|CF349127
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTA
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTA
EST: gi|211540781|gb|FL336428.1|FL336428
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|71311903|gb|DR792430.1|DR792430
EST:     AGGCGTTGAGA-TGACCCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: AGGCGTTGAGATTGA-CCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|108823920|gb|EC277928.1|EC277928
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCCGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|148937230|gb|EC881412.2|EC881412
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
EST: gi|211318389|gb|FL341246.1|FL341246
EST:     TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG                         GTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT
genomic: TGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGAT

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: 340

GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3154

GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2768

GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 518

GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAGgttatctttt ... gtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttcagtttattttgagtaatttaaatgtttgtttcaatgttgtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT
                                              tctattt  CT-rich tract
         tttattttgagtaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcttttctttcttccctagctttctcttctttgcctgtggggcgtatttacacctgtccaccgataaatctgattgagattgtattgggaagttgaatttatcactaacacaagtttcagtttattttgagtaatttaaatgtttgtttcaatgttgtctatttagGTTGACGAATATTCTCGTACTTCTGCTCCTAGTGTATGGGCTGTGGGTGATGTAACAAACCGGATTAATTTAACACCTGTTGCATTGATGGAGGCAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG