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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaattagtttgttcactatttatcatatgaagtactcacatagacacatactatagaatttgccatttatttatgccttctgatgttgctttgagtttcttgctatgttttatcttgacgtccagcaaaggcccattgaacatattagaagtaaatacaacatgttaactgataggtaacatttttttacag

Basic information

species Zea mays
transcript GRMZM5G856653_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856653_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g53930.2 (Oryza sativa), 5'ss of exon 4
GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaattagtttgttcactatt-tatcatatgaagtactcacatagacacatactatagaatttgccatttatttatgccttctgatgt-tgctttgagtttcttgctatgttttatcttgacgtccagcaaaggcccattgaacatattagaagtaaatacaacatgttaactgataggtaacatttttttacag
|| || ||||||||||||||||||||||| ||||| ||||||||||| || ||||||||||||||| ||||||| |||| ||||||  || |||||  | | | | | |   | |  |||  |  |    | | ||      ||| | |  | |||||     | |   | | |||                                                                                                   
GTGGGGGAAGATGTTGTGGCTGAATTGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaattc-ttggttcatgactctgttaaaattatttatcatctgaaactttcccatg---cctgctactgctatatgctgatgggtaaatacattggca------------------------------------------------------------------------------------------------
















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|148957702|gb|EC903823.2|EC903823
EST:     TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG                         GTTAATGATACTGTAGGCACA
genomic: TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACA
EST: gi|211232468|gb|FK968372.1|FK968372
EST:     TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG                         GTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
genomic: TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
EST: gi|148980000|gb|EE026913.2|EE026913
EST:     TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG                         GTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
genomic: TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
EST: gi|148933666|gb|EC877560.2|EC877560
EST:     TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG                         GTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
genomic: TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
EST: gi|211232471|gb|FK968375.1|FK968375
EST:     TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG                         GTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
genomic: TGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
EST: gi|211437009|gb|FL298821.1|FL298821
EST:     GTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG                         GTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT
genomic: GTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGAT

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), 45 (downstream exon)
Score: 149

GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGATGTTGTTGCTGCTGTAATATTGGGCACTGGCACAAATGCAGCTTATGTGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 197

GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGATGTTGTTGCTGCTGTAATATTGGGCACTGGCACAAATGCAGCTTATGTGG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 69

GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGATGTTGTTGCTGCTGTAATATTGGGCACTGGCACAAATGCAGCTTATGTGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 138

GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaat ... ttttttacagGTTAATGATACTGTAGGCACATTGGCTGGTGGGAGATATGCTGATAATGATGTTGTTGCTGCTGTAATATTGGGCACTGGCACAAATGCAGCTTATGTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaattagtttgttcactatttatcatatgaagtactcacatagacacatactatagaatttgccatttatttatgccttctgatgttgctttgagtttcttgctatgttttatcttgacgtccagcaaaggcccattgaacatattagaagtaaatacaacatgttaactgataggtaacatttttttacag

- - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC