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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccccccgacctccgaactccacctagagttgtactcgcgcgggttcgcttacctctgcgttgctctggaaaaattcccaactcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTGTCGTTCACGCTCGACGACGGCACCGGGAAGATCGCGCTCACGCGGTG

Basic information

species Zea mays
transcript GRMZM2G018946_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018946_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g47830.1 (Oryza sativa), 3'ss of exon 2
gtaagccccccg--acctccgaactccacctagagttgtactcgcgcgggttcgcttacctctgcgttgctctggaaaaattcccaactcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTGTCGTTCACGCTCGACGACGGCACCGGGAAGATCGCGCTCACGCGGTG
||| ||  | ||  ||||||  |     |||  | || |  || || ||   ||| ||  ||||  ||  | |||     | ||      |  | |||||| || || |||||||||||||||||||||||| || |||  |   |||||  ||||| ||||| ||| |||||||||||||| | |||   |||||
gtaggctactcggcacctccacagcttccctcaatttattttc-cgtggccccgcgtaa-tctgtttttttttggg----tgccgttgatggttttagGTTAGGGTTTTGGGGAGGGTGGTGAGCGTGGTGAGCAGGGATACTGACGTGTGCTTCACTCTCGATGACAGCACCGGGAAGATCCCACTCGTTCGGTG
















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|78091533|gb|DV519907.1|DV519907
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|76915058|gb|DV165799.1|DV165799
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|71442030|gb|DR823080.1|DR823080
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|93013550|gb|EB639070.1|EB639070
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|71435524|gb|DR816574.1|DR816574
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|91049845|gb|EB160263.1|EB160263
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCG
EST: gi|91876766|gb|EB406723.1|EB406723
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|78088916|gb|DV517309.1|DV517309
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|31558428|gb|CD527640.1|CD527640
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|71419272|gb|DR804704.1|DR804704
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
EST: gi|71446837|gb|DR827887.1|DR827887
EST:     CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAAC                         GTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG
genomic: CCGGTGATGGCGACCTTGTCATCCCTATCGACGGCGTCGACGCCACCAACgtaagccccc ... tcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcgggttcgcttacctctgcgttgctctggaaaaattcccaactcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTGTCGTTCACGCTCGACGACGGCACCGGGAAGATCGCGCTCACGCGGTG
         cgcttac  putative branch site (score: 3)
                                aaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccccccgacctccgaactccacctagagttgtactcgcgcgggttcgcttacctctgcgttgctctggaaaaattcccaactcgcgtgtagGTTTGGATTCTGGGGAGGGTGGTGAGCGTGGTGAACATGGAGGCCAGCGTGTCGTTCACGCTCGACGACGGCACCGGGAAGATCGCGCTCACGCGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA