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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttcttgcctatgatatgttatgttgcttctgtgaagtgctgctttcgtagcttcttagcttgtgttgtgccttgtaatggaattacttgccttcactgatctgttttgtatttttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG

Basic information

species Zea mays
transcript GRMZM2G123732_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123732_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
--------gtaccttcttgcctatga---tat-gttatgttgcttctgtgaagtgctgctttcgtagcttcttagcttgtgttgtgccttgtaatggaattacttgccttcactgatctgttttgtatttttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG
        ||| |||||   |||| |   |||   || | |||||   |||  |  | | || | |  ||||  |       |    ||| || | |  || |||  | |||   ||   |  |  || | |  |||||||||||||| ||||||||||||| ||| ||||| || || ||||| || |||||||||||||||||||||||||||| ||| |  | |||  |||  ||||
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttata-tagcttttctt--catcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG
















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|211324995|gb|FL127007.1|FL127007
EST:     GACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: GACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
EST: gi|211118164|gb|FL349423.1|FL349423
EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGGAAGACATGCTCCTA
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGG-AAGACATGCTCCTA
EST: gi|211474975|gb|FL438616.1|FL438616
EST:     CGCTTTACCTTCCCCTCCCATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
EST: gi|74244183|gb|DT652097.1|DT652097
EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
EST: gi|33092349|gb|CF052343.1|CF052343
EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
EST: gi|93011727|gb|EB637247.1|EB637247
EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
EST: gi|32933373|gb|CF038185.1|CF038185
EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
EST: gi|32934905|gb|CF039717.1|CF039717
EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

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), 43 (downstream exon)
Score: 80

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 72

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 55

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttgtaatggaattacttgccttcactgatctgttttgtatttttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG
                         cactgat  putative branch site (score: 55)
                                        tattttt  putative PPT
                                 tgttttgtatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttcttgcctatgatatgttatgttgcttctgtgaagtgctgctttcgtagcttcttagcttgtgttgtgccttgtaatggaattacttgccttcactgatctgttttgtatttttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG