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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaaatgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag

Basic information

species Zea mays
transcript GRMZM2G149321_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g40340.2 (Oryza sativa), 5'ss of exon 16
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaa--atgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag
||||| |||||||||||||||||||| ||||| |||||||||||  |||| ||||||||||| |||||  ||||||||   ||||  ||  ||  | ||  | | || |||||| |||  | |  |    ||||||  | ||||| |||| ||||||
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttg--ggctaattatgtgtttatgtatttaaaagcag

upper sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 16
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaaa--tgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag
||||| |||||||||||||||||||| ||||| |||||||||||  |||| ||||||||||| |||||  ||||||||   ||||  |||  |  | ||  | | || |||||| |||  | |  |    ||||||  | ||||| |||| |||   
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttg--ggctaattatgtgtttatgtatttaaaag---

upper sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G13580.1 (Glycine max), 5'ss of exon 18
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttac-tatctcgaaatgttctgtcacccttagtttt-tatgtgatggctgatagattatgcatgtatgtgtttataagcag-------------------------------------------------------
||||| ||||||||||||||||| || || ||||| ||||||||||||||  ||||||||||||| || |||||| |    |  |||      |  |       | | |||| ||  |  |   |||    | |||| ||  |||  | ||    ||                                                       
GATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAGgtaaatggtgtgcctctgttgatcatacatgtgtcaattttctactttgtatttgaactgtcatgcctg-gtgt-ctcatgtaaaggtctttattccaattctttcaatgtataccttagattttgctttgacacatgcag

upper sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 18
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaaatgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag----------------------------------
||||| || |||||||||||||| || || || || ||||| || ||||| || |||||||||||||| |||||||    |      || |||| | ||    |     || ||  | ||  |   |   ||||| ||    || |  |   |                                    
GATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAGgtaatcggtt-----caactgttttttcctggtagaaattaatccgttgattcgcatcatatgcttgagcttgat-gtggtcccttaacttacgaaatataacatggtgtcgttgcag

upper sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 5'ss of exon 18
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaaatgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag-----------------------
||||| || |||||||||||||| ||||| ||||| ||||||||| ||||  |||||||||| ||||| |||||  |      |      | || ||  ||| |    || ||| ||||  || ||  |  ||| |   |       | |||||                        
GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAGgtaggtggaagccct----tattttg--accttctccttctatatgatacct-atttaaaatgaaaaaaaaaaaaaaaaagcaatctgaaggtcttctccattgtcc

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|67016491|gb|CO445240.1|CO445240
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG                         CTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
EST: gi|211428993|gb|FL402814.1|FL402814
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG                         CTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
EST: gi|31364305|gb|CD448660.1|CD448660
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCATGACAG                         CTCCCTGTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
EST: gi|211266310|gb|FL390568.1|FL390568
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG                         CTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT

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: 384

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 296

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaaatgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag

- - - - - - - - - -  TCAGCT
- - - - - - - - - - - CAGCTG
- - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG