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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttctcttctttgcttatcccacagatttcctgtggttatgtatccatctgggcaacaaactcagaactaaacacattttttgttaaatgtgattttatcag

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 5'ss of exon 7
TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttctcttctttgcttatcccacagatttcctgtggttatgtatccatctgggcaacaaactcagaactaaacacattttttgttaaatgtgattttatcag
||||||||||||||| || |||||||||||||| || ||||| |||||||||||||| ||||||||||| ||||||||||||||| |||| ||||||||||||| || || ||  | |||| |   || | |||  | |       |  | ||      | ||||||  ||||||||||  ||||||||  |      ||||  |||
TTACCGTGCTCCAGAACTGATATTTGGGGCAACCGAATACACGACATCAATTGATATATGGTCAGCTGGGTGTGTTCTTGCTGAGTTGCTCCTTGGCCAGgttatttcctgtttgtggcttctttgactgtttttttttatcaggttgactat------agcaaactttgaactaaacatcttttttgtcca------tttttccag

upper sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 8
TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgtta-gtttctcttctttgcttatcccacagatttcctgtggttatgtatccatctgggcaacaaactcagaactaaacacattttttgttaaatgtgattttatcag
|||||||||||| || || |||||||| |||||||| ||||||||| | || || || |||||  ||||||| ||||| |||||| | |||||||| ||||||   |  ||| || ||||   ||       || | |   |  |   | || |||   |||  |  ||   |||   ||                            
TTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCTGGTCGACTGGATGCGTTCTGGCTGAGTTACTTCTTGGTCAGgttgtatacctcgtccttgcaactc-------ttccattatgccactca-ccgtctcatcaatcatttcc--actgtgcag---------------------------

upper sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 8
TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgtta-gtttctcttctttgcttatcccacagatttcctgtggttatgtatccatctgggcaacaaactcagaactaaacacattttttgttaaatgtgattttatcag
 ||||||||||| || || |||||||| |||||||| ||||||||| | || || || |||||  ||||||| ||||| |||||| | |||||||| ||||||   |  ||| || ||||   ||       || | |   |  |   | || |||   |||  |  ||   |||   ||                            
CTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCTGGTCGACTGGATGCGTTCTGGCTGAGTTACTTCTTGGTCAGgttgtatacctcgtccttgcaactc-------ttccattatgccactca-ccgtctcatcaatcatttcc--actgtgcag---------------------------

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|19770441|gb|BQ035162.1|BQ035162
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|148932530|gb|EC876330.2|EC876330
EST:     TGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTTGGC-AG                         CCTCTCTTCCCTG
genomic: TGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTT-GGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTG
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|71441697|gb|DR822747.1|DR822747
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|32855414|gb|CD995095.1|CD995095
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|211298028|gb|FL233897.1|FL233897
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|211326797|gb|FL341548.1|FL341548
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|211298026|gb|FL233895.1|FL233895
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
EST: gi|20300401|gb|BQ163344.1|BQ163344
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG

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: 236

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttct ... attttatcagCCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttctcttctttgcttatcccacagatttcctgtggttatgtatccatctgggcaacaaactcagaactaaacacattttttgttaaatgtgattttatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT