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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcag

Basic information

species Zea mays
transcript GRMZM2G053764_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T06 (Zea mays), 5'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 5'ss of exon 1
GCGAGGAGCTGAGGGG-GGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggat-gctggacctc---tcttggtctgttttccaattctgcctgaccgtg--------ttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcag
  |||  || | | ||  || |        || |     |   |  |||   | |  ||||| |||||||||||||||||||| |||||  | ||||| |||||||  | ||     |||   | |   |   || | |  |      || |  ||         |||   | |  ||| ||    ||||   |||| ||||    | | || | ||  |      | |  |||
-TGAGCGGCGGGGCGGCAGGGCAGGGCAGGGCAGCAGCAGCAGCAGCGCAGGCGAGAATGTCTTCCCCGAGCAAGCGCCGCGAAATGGATGTGATGAAACTgtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccag

upper sequence: GRMZM2G053764_T06 (Zea mays), 5'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 1
GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggat-gctggacctc---tcttggtctgttttccaat-tctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcag
                                                        ||||| |||||||||||||||||||| |||||  | ||||| |||||||  | ||     |||   | |   |   || | |  | ||     ||||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||
--------------------------------------------------------ATGTCTTCCCCGAGCAAGCGCCGCGAAATGGATGTGATGAAACTgtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccag
















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|211363205|gb|FL271919.1|FL271919
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|32859414|gb|CD999095.1|CD999095
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|50325609|gb|CO520735.1|CO520735
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|94476395|gb|EB705353.1|EB705353
EST:     TCCCAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     CCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: CCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|211174889|gb|FL306344.1|FL306344
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 709

GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 914

GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGGAGCTGAGGGGGGGCCCTTCTGCTGCTGTTCTTGTTTCCCCGCTCTCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC