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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatgattcttttgcagaaacaaatgtttgaaaacaaaataagattaacattattaattgttgaagtgtataaatggattgattgccttctcccac...

Basic information

species Zea mays
transcript GRMZM2G149272_T06
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g42520.2 (Oryza sativa), 5'ss of exon 9
TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatg-attcttttgcagaaacaaatgtttgaaaacaaaataagattaacattattaattgttga-agtgtataaatggattgattgccttctcccac-
|||| | ||||| || ||||||||| ||||||| ||| ||||||||||||||| ||||||||||||||||||||  || ||||| || ||||||   ||||||   |   | | | ||| |||| ||||  |   ||   ||||    |||   ||| | | ||    | | |  || ||     |||    | ||       
TGCACTACTTCTGTCTGGAAGAACATTGAAGGGGTCTTTGTTTGGAGGATGGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagacaatgtgttgtagaagcaaacatcctaa--taaaactgaattc-tattttcagttaaaaatattaaattaagaagctgaacttcatcatatgta

upper sequence: GRMZM2G149272_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA09G29070.1 (Glycine max), 5'ss of exon 9
TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatgattcttttgcagaaacaaatgtttga--aaacaaaataagatta-acattattaattgttgaagtgtataaatggattgattgccttctcccac
||   | || |||   ||||||||| |||| |||||| | ||||||||||||||||||||||||||||| |||||||| || || || |||      ||||||  |   |   |     | | ||      ||     ||||  |  |  ||| | ||| ||| |   | |  || |     | | ||  | |||||| |   
TGGGCTACTCCTAATGGGAAGAACATTGAAAGGATCTCTATTTGGAGGATGGAAACCTAAATCTGATCTTCCTTCATTAGTAGAGAAGTATCTCAACAAGgtaactgcaacagtacccaaaatacttcctcttatctgaacatgactactttatatatttttactc--taagctgaaacgtagcaatgtctaccttctgcat-

upper sequence: GRMZM2G149272_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G23820.1 (Glycine max), 5'ss of exon 11
TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatgattcttttgcagaaacaaatgtttgaaaacaaaataagatta-acattattaattgttgaagtgtataaatggattgattgccttctcccac-
|| | | || |||   ||||||||| |||| |||||| | ||| | ||||||||||| ||||||||||| |||||||| ||  | || ||       ||||||  |   |   | |  | | |         |   |||   |  |  ||| || || | | |   | |  || |  |  | | ||  | |||||| |    
TGGACTACTCCTAATGGGAAGAACATTGAAAGGATCTCTATTTTGGGGATGGAAACCAAAATCTGATCTGCCTTCATTAGTAAAGAAGTACCTCAACAAGgtaactgaaacagtatacccggattcctctcatctgaacctgactactttatacgttttcactc--taagctgaaacacggcaatgtctaccttctgcataa

upper sequence: GRMZM2G149272_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv16s0039g00320.t01 (Vitis vinifera), 5'ss of exon 9
TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatgattcttttgcagaaacaaatgtttgaaaacaaaataagattaacattattaattgttgaagtgtataa-atggattgattgccttctcccac---------
|| |||  |||| || ||||||||  |||  |||||| | ||||||||||||| ||||||||||||||| | |||||| || || |  |||      ||||||   |  |   ||      || |  |   | ||   ||   | |  ||       ||| |||||    | ||||  |||  |||| | |   ||| ||          
TGGATTATTTCTTTCTGGAAGAACGTTGAGAGGATCTTTATTTGGAGGATGGAGACCTAAATCTGATCTTCATTCATTAGTAGACATGTATATGAGGAAGgtaagaaccacaatt------aatcttacagtggatttcagcctgaattttctcactttatttgtt----tttataccatgtcttgacttctgcctctcaaagcttcact

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|5608335|gb|AI902107.1|AI902107
EST:     GAAACCTAAATCTGATTCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GAAACCTAAATCTGA-TCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5325210|gb|AI783401.1|AI783401
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|67012049|gb|CO440798.1|CO440798
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|6342730|gb|AW165554.1|AW165554
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211322359|gb|FL445870.1|FL445870
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5895724|gb|AW036970.1|AW036970
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|94474409|gb|EB703367.1|EB703367
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5860434|gb|AW011656.1|AW011656
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCGGGGGATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|84969909|gb|DW468311.1|DW468311
EST:     ATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: ATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5650119|gb|AI920479.1|AI920479
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|148957214|gb|EC903224.2|EC903224
EST:     TCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: TCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|67013266|gb|CO442015.1|CO442015
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211242574|gb|FL481994.1|FL481994
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211240359|gb|FL481993.1|FL481993
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211242575|gb|FL481995.1|FL481995
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatgattcttttgcagaaacaaatgtttgaaaacaaaataagattaacattattaattgttgaagtgtataaatggattgattgccttctcccac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG