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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtaaaggatccatcatttttttccattttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG

Basic information

species Zea mays
transcript GRMZM2G035150_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g64219.3 (Oryza sativa), 3'ss of exon 4
gt-ttgtgtaaaggatccatcatttttttccattttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG
|| ||   | ||  ||  |   ||||| || |||||            |||     |||| ||| ||   |||  |||  || |||||| |||||  |||| |||||||||||||| ||  ||||||| ||||||||||| ||||| ||| | ||||| |||
gtattacttcaaatatgtactctttttctctattttatg---------ctctacttatctcttt-tagcatgta-tcttatacacagTTCCGAGCATTGTCCGATCAATTTTACCGCACCACTGAACACCACAGATTTGTTCGGCAACAAATAGTGAAACAG
















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|71427954|gb|DR809004.1|DR809004
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGGTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|88748647|gb|DY532788.1|DY532788
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|74235679|gb|DT643593.1|DT643593
EST:     GGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGGCA-CTGCCAG                         TTTCGAGCGCTGT
genomic: GGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGG-CAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGT
EST: gi|71763432|gb|DR961369.1|DR961369
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|76291810|gb|DV031378.1|DV031378
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG
              atctcac  putative branch site (score: 3)
                                           tctctt  putative PPT
                           tatttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtaaaggatccatcatttttttccattttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC