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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgagtgattagtaatgctggagatgcaaaatttcttcttttcttgcgtaaacatacatactataaatttatactgatctgtttttacccttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTTATTGAGCTCATGCCAAAATTGGGACAACACTTTGTTGAAGAAATGATAA

Basic information

species Zea mays
transcript GRMZM2G047223_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 5
tttgagtgattagtaatgctggagatgcaaaatttcttcttttcttgcgtaaacatacatactataaa-tttatactgatc-------tgtttttacccttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTTATTGAGCTCATGCCAAAATTGGGACAACACTTTGTTGAAGAAATGATAA
     |  ||| || ||| || | || |||  ||| | |  | | ||   || | | |||| | ||||  | ||||||| |       ||||| ||  |||| |||||||||||||||||||||||||||||||| ||| ||||||||||||||||||| | ||||  |||||| | |||||||| || ||| |||||||||||||||
-----gcaattggtgatggtgcatatacaa--tttttacactacatgaa-aagcctgcatattctaaagctaatactgaacaaactactgtttatattcttgcaacagGCTGGTTTGCCGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAA
















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|78113905|gb|DV532294.1|DV532294
EST:     TCGCATTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGT
EST: gi|71771757|gb|DR969694.1|DR969694
EST:     CTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
genomic: CTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
EST: gi|89247292|gb|DY619078.1|DY619078
EST:     TCGCATTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
EST: gi|61118400|gb|DN559361.1|DN559361
EST:     TCGCTTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
EST: gi|78118514|gb|DV536898.1|DV536898
EST:     TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
EST: gi|91874336|gb|EB404293.1|EB404293
EST:     TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCT
EST: gi|78113904|gb|DV532293.1|DV532293
EST:     TCGCATTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAG                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
EST: gi|78118515|gb|DV536899.1|DV536899
EST:     TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAN                         GCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT
genomic: TCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggcta ... cttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtaaacatacatactataaatttatactgatctgtttttacccttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTTATTGAGCTCATGCCAAAATTGGGACAACACTTTGTTGAAGAAATGATAA
                           tactgat  putative branch site (score: 2)
                                 tctgtttttaccctt  CT-rich tract
     aaacatacatactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgagtgattagtaatgctggagatgcaaaatttcttcttttcttgcgtaaacatacatactataaatttatactgatctgtttttacccttggaacagGCTGGTTTGCCGCTTGTGCAGCAATATTTGTCTCAGTTTGAGAAATTAGTTATTGAGCTCATGCCAAAATTGGGACAACACTTTGTTGAAGAAATGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - aatgctg
- - - - - - - - - - - -gatgcaa
- - - - - - - - - - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - acataca