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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgcacatgtgcatgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag

Basic information

species Zea mays
transcript GRMZM2G020446_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 2
GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgcacatgtgcatgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag
|| || ||||||||||||||||||||||||| ||||| |||| | |||| |||||||| ||||||||||| | ||||| |||||||||||||| |||||| ||| | | || || | || || | | || | | | | | | || || | || |||| | |||||| | || | |
AGACAGTGAATTTGATTTGGAGAATATTGTCACTGCTGCGAGAGTTGCTGGGAAGAAAGTCCCTGTTTTGCTCAGGATAAACCCAGATGTGGATCCACAGgtaaagtttttc-ctcccacctcaggatacagtgggggatttagttatat-tggtatgctattgtgttattgtcatataat-actagaaatcagattatatag----

upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0070g00580.t01 (Vitis vinifera), 5'ss of exon 2
GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatg-gttatcctctagtactccccaatgcacatgtg-catgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag
||||| |||||||||||||| |||||| | |||||||||| | |||| ||||| || |||||| ||| | || ||||||||||||||||| |||||||| | | || | || | | | || | | | | || ||| | | || ||| | | |||| || |
TGATAGTGAATTTGATTTGGATAATATTATATCAGCTGCAAGAATTGCTGGCAAGAAGGTCAATGTTTTACTTAGGATCAATCCAGATGTGGATCCTCAGgtatgtgctgtcattgtttaattctaatgttacgaataatgtaatgttgtagggtgttcat-agaacaggtatttcccttaggttgggtaaatttggttat--------

upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g04490.t01 (Vitis vinifera), 5'ss of exon 2
GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgc-acatgtg-catgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag
||||| |||||||||||||| |||||| | |||||||||| | |||| ||||| || |||||| ||| | || ||||||||||||||||| |||||||| | || | | |||| || | | | | || ||| | | | ||| | | |||| || |
TGATAGTGAATTTGATTTGGATAATATTATATCAGCTGCAAGAATTGCTGGCAAGAAGGTCAATGTTTTACTTAGGATCAATCCAGATGTGGATCCTCAGgtatgtgctgtcactgtttaattctaatgttacgaataatgtaatgttgtagggtgttcat-agaacaggtattgcccttaggttgggtaaatttggttat--------

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|20208183|gb|BQ134272.1|BQ134272
EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
EST: gi|148934359|gb|EC878388.2|EC878388
EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATC
EST: gi|211003081|gb|FL282330.1|FL282330
EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCACAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCCG
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCC-G
EST: gi|50329919|gb|CO525045.1|CO525045
EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCTTATGTTGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGC
EST: gi|9825116|gb|BE575318.1|BE575318
EST:     TAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
EST: gi|26456264|gb|CA827847.1|CA827847
EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCGCATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
EST: gi|211452559|gb|FL415488.1|FL415488
EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCACAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
EST: gi|166441682|gb|EG195243.1|EG195243
EST:     CAGATGTGGATCCGCAG                         GTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: CAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC

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: 257

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGCAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGCAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGCAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGCAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgcacatgtgcatgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG