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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttcttctcagcattaacgtcgttaaagtgtgttttttttgcttgttcagttctaattttatatttgttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG

Basic information

species Zea mays
transcript GRMZM2G079668_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079668_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g23740.1 (Oryza sativa), 3'ss of exon 4
----------------------------------gttcttttcttct-cagcattaacgtcgttaaagtgtgttttttttgcttgttcagttctaat--tttatatttgttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG
                                   || |  | ||   | |  |     | | ||       |||  ||  |||| |   ||||||   ||  |  |  ||||||||| || || || |||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||||||
gttagcttgcttgaccgccttgatttgctgcagcattgtgctattggactgtttccttttgggtagcaatcctttgattcccttggttgattctaaccattggttatgcttctttcagTTTACCCTTCATTACAGCTACTGCTGATGGGCCCAAGCATATCGAGACAACTCTTACCAGGGCTAAATTTGAGGAGCTATGTTCAGATCTTCTTGACAG
















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|71446645|gb|DR827695.1|DR827695
EST:     GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
genomic: GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
EST: gi|211464630|gb|FK976061.1|FK976061
EST:     GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGCCTTTTATTACAGCTACTGCAGATGGNCCCAAGCATATTGAGACTAC
genomic: GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
EST: gi|87153250|gb|DY398039.1|DY398039
EST:     GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
genomic: GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
EST: gi|67039401|gb|CO465656.1|CO465656
EST:     TGAGAAGG-ACAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
genomic: TGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
EST: gi|71761337|gb|DR959274.1|DR959274
EST:     GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGTCTTTTATTACAGCTACTG
genomic: GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTG
EST: gi|22490415|gb|BU050338.1|BU050338
EST:     GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
genomic: GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
EST: gi|78080017|gb|DV508429.1|DV508429
EST:     GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAG                         CTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC
genomic: GCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTAC

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: 108

GTATTGATTTGCTAAAAGATAAGCAAGCACTGCAGCGATTGACAGAAGCAGCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

GTATTGATTTGCTAAAAGATAAGCAAGCACTGCAGCGATTGACAGAAGCAGCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 29

GTATTGATTTGCTAAAAGATAAGCAAGCACTGCAGCGATTGACAGAAGCAGCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 276

GTATTGATTTGCTAAAAGATAAGCAAGCACTGCAGCGATTGACAGAAGCAGCTGAGAAGGCAAAGATGGAACTGTCATCTTTGACCCAAACAAACATGAGgttcttttct ... gttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaaagtgtgttttttttgcttgttcagttctaattttatatttgttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG
                             ttctaat  putative branch site (score: 276)
                                          tttgttctttc  putative PPT
                             ttctaattttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttttcttctcagcattaacgtcgttaaagtgtgttttttttgcttgttcagttctaattttatatttgttctttcagCTTGCCTTTTATTACAGCTACTGCAGATGGTCCCAAGCATATTGAGACTACTCTTACCAGGGCTAAATTTGAAGAGCTATGCTCAGATCTCCTTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT