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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgttcttttcaattttcagctgtttaagattaacatccatgatgtgtttaatactgagttgcatgtaatatgccag

Basic information

species Zea mays
transcript GRMZM2G029566_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 7
GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgttcttttcaattttcagctgtttaagattaacatccatgatgtgtttaatactgagttgcatgtaatatgccag
|| ||||||||||| |||||||||||||| || |||||||| ||||||||||| || ||||||||||| ||||||||||   | |||||||||||||||||||   | ||||||||| |||||      || |||| |   | |||  | || |||| ||||||||   | ||||||  |||
GCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTGgtagg-tattcttttcagttttcg-----ttcagatcagt-tgcatactttggttaa-actgagttttgtataatattgcag
















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|211126134|gb|FL125776.1|FL125776
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|71328229|gb|DR800748.1|DR800748
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTG
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTG
EST: gi|148969714|gb|EE020586.2|EE020586
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTT
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTT
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|60348819|gb|DN215792.1|DN215792
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|71328227|gb|DR800747.1|DR800747
EST:     GGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTGGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: GGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|78124352|gb|DV542736.1|DV542736
EST:     GAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: GAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|148940815|gb|EC885642.2|EC885642
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAAATATCCAG
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAG
EST: gi|148964333|gb|EC905725.2|EC905725
EST:     TGACGCCGAAGAACATATTTTTGGGCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCT
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCC-AGGCTTGGGAGACTATACCTCTTGGACCTTTCCT
EST: gi|60346412|gb|DN213385.1|DN213385
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|78124353|gb|DV542737.1|DV542737
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGAGAGACTATACCTC
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTC
EST: gi|148956082|gb|EC901838.2|EC901838
EST:     TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCT
genomic: TGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCT
EST: gi|86465953|gb|DY232326.1|DY232326
EST:     CGAAGAACATATTTTTTGCCTAACTTTGATGAATGATTGGAGTG                         CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTT-CTTTGGA
genomic: CGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA

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: 334

GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 439

GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2010

GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgtt ... aatatgccagCCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTGgtattctgttcttttcaattttcagctgtttaagattaacatccatgatgtgtttaatactgagttgcatgtaatatgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG