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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatgctcaccagtcaccatttacatgaaatttgcttttgactgctaatgcacttgacaaactaaaatctggcctttcctgatcttttctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGGGATGATGGAATATAAACTTTGGATGATGTCAATTATATCTTAGGTTCCT

Basic information

species Zea mays
transcript GRMZM2G035595_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 7
----taaaatgctcaccagtcaccatttacatgaaatttgcttttgactgctaatgcacttgacaaactaaaatctggcctt--tcctgatcttttctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGGGATGATGGAATATAAACTTTGGATGATGTCAATTATATCTTAG--GTTCCT
    | ||||  | |||| | | | | |    ||||   |  | |||    | | |   || |     | |  | | ||| |   |   || |||||| |||||||||||| || || || ||||| || || ||||  |||||||||||  ||||||||||||||| ||| ||| || | ||      ||     ||||   || | 
cttgtgaaattgt-acca-ttatcctgtttgcgaaaa--gtctctgagaattcaggt--ttcatgcttttatttttagccataacctatatattttcttaatgcagGTTACACTTGTAAAGATGGTAAACGAGGCTACCGCAAACCTTCCAGGGTGGGATGATGGAAGATAGACTATG-ACGACAAATGTTGCTGATTAGTGATTAC-
















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|5928606|gb|AW056003.1|AW056003
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|211142481|gb|FL118078.1|FL118078
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|71441274|gb|DR822324.1|DR822324
EST:     CACCCCCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTTTAGTGAAAATGGTCAATGAAGCTAGTGCAACCCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|148949122|gb|EC894553.2|EC894553
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|211025730|gb|FL435838.1|FL435838
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|211541587|gb|FL476015.1|FL476015
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|71759438|gb|DR957375.1|DR957375
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|211246948|gb|FL479530.1|FL479530
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|86472181|gb|DY238551.1|DY238551
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|149009585|gb|EE154018.2|EE154018
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTTTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|5928615|gb|AW056012.1|AW056012
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|5816276|gb|AI987192.1|AI987192
EST:     CCCCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|84970100|gb|DV171467.2|DV171467
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
EST: gi|4776320|gb|AI665323.1|AI665323
EST:     CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTG                         GTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG
genomic: CACCACCAAGAAATCTTACATTGCCCCCTCCTGGAGTACCAGAAAGTGTGgtaagtgtat ... ctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaatgcacttgacaaactaaaatctggcctttcctgatcttttctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGGGATGATGGAATATAAACTTTGGATGATGTCAATTATATCTTAGGTTCCT
                             cctttcctgatctttt  CT-rich tract
               aaactaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatgctcaccagtcaccatttacatgaaatttgcttttgactgctaatgcacttgacaaactaaaatctggcctttcctgatcttttctcaatgcagGTTACTCTAGTGAAAATGGTCAATGAAGCTAGTGCAAACCTTCCTCGGTGGGATGATGGAATATAAACTTTGGATGATGTCAATTATATCTTAGGTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA