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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAACTTCGATCTTAACCACATCGATGTAGCCGTTGTGCTGAATTTCTTGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtttcttaattctgatactcccatttacacactgtacaactgtcttgattggatcagtcggcagccaaaactaatgttctttattatatataccattggcag

Basic information

species Zea mays
transcript GRMZM2G027851_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 6
CCAGAACTTCGATCTTAACCACATCGATGTAGCCGTTGTGCTGAATTTCTTGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtttcttaattctgatactcccatttacacactgtacaactgtcttgattggatcagtcggcagccaaaactaatgttctttattatatataccattggcag
 |||||||| ||||||  |||||| ||||  || || || ||||| |||||||| ||||||| ||| |||||  |||| |||||||| |||||||| ||||||||||| ||||||| | | |     |  ||||||   |      ||||||||| |  |    | ||  | || |  |||   |   |||| |   | |     ||||
ACAGAACTTTGATCTTGTCCACATAGATGCGGCTGTCGTTCTGAAATTCTTGGGGAACTTCTTTTATTTATTTTTGTCGAGCACCTTCCTTGGAGTATTTgtaagttgattcttaagtttca-----ctttttacatcttac-tgtctgtcttgactctactgcttggttgacacatgtaa-acttaatattcttcttccaccctgcag
















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|74239375|gb|DT647289.1|DT647289
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTAT
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTAT
EST: gi|71437105|gb|DR818155.1|DR818155
EST:     GGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: GGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|71446906|gb|DR827956.1|DR827956
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|50333105|gb|CO528231.1|CO528231
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAG
EST: gi|78080130|gb|DV508542.1|DV508542
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|74238599|gb|DT646513.1|DT646513
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGTCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|211100374|gb|FL186479.1|FL186479
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|93282181|gb|EB674445.1|EB674445
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|78093453|gb|DV521827.1|DV521827
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTT                         ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG
genomic: TGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtt ... ccattggcagACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAACTTCGATCTTAACCACATCGATGTAGCCGTTGTGCTGAATTTCTTGGGAAACTTCTGTTACTTATTCGTGTCAAGCACCTTACTTGGAGTGTTTgtaagttgtttcttaattctgatactcccatttacacactgtacaactgtcttgattggatcagtcggcagccaaaactaatgttctttattatatataccattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG