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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcggttgtctcatctgttctagtacatgataatctccatacgctgcagaatggaaatggtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG

Basic information

species Zea mays
transcript GRMZM5G838196_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G838196_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 3'ss of exon 4
gtaggcggt----tgtctcatctgttctagtacatgataatctccatacgctgcagaatggaaat----ggtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG
|||||   |    ||  || ||  | | |  || |   |||||  | || |   |||       |    |||| |  |  |  |      |         |  | |||| ||| | | |   |||||||||||||||||||||||||| | ||||||||||||||| |||||||| ||||| ||||||||||||||| | |||||||||||
gtaggttctttgatgcttcttcattacaatcactttgcaatctgaaaacaccttagatcatctttcacaggtaacattacaattctttattactgagtgttttctttttgtgatcca-tgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG
















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|211467385|gb|FL438566.1|FL438566
EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
EST: gi|148962266|gb|EE013089.2|EE013089
EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGGGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
EST: gi|13557980|gb|BG549336.1|BG549336
EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
EST: gi|211164012|gb|FL463865.1|FL463865
EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
EST: gi|211164011|gb|FL463864.1|FL463864
EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
EST: gi|211467384|gb|FL438565.1|FL438565
EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG
                                     ttctgac  putative branch site (score: 2)
                                               ctccc  putative PPT
                                  attttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcggttgtctcatctgttctagtacatgataatctccatacgctgcagaatggaaatggtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC