Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttactgcctgcctttttatcatctctgcctccttgttctcatatgcccctgattcatcgaggctgaaatcgtgttttttctgtctgttgtgaactgcggaaaag

Basic information

species Zea mays
transcript GRMZM2G167872_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 6
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttactgcctgcctttttatcatctctgcctccttgttctcatatgcccctgattcatcgaggctgaaatcgtgttttttctgtctgttgtgaactgcggaaaag
||| || || || |||||  |||| ||||| ||||| |||||||| |||||||| ||||| ||||| ||||||||||| |||||||||    |||||||||||||||  |  |||  | | | |  |  ||     ||| | || | ||   |||  ||  | ||  ||||||| ||||  ||| ||||    |               
TCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGATTgtatgtt-ttctctgtttatctttacttcctttgctcttatgct-agatttaccttgttagttgaa-ctgaaat-gtgtactttatgtcaaaag---------------

upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 6
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgtt--actgcctgccttt-ttatcatctctgcctccttgtt------ctcatatgcccctga-----ttcatcgaggctgaaatcgtgtt------ttttctgtctgttgtgaactgcggaaaag
||| ||| |  |||||||  | |||||||| || || |||||||| |||||||||||||| ||||| || ||||| || ||||||||  |||||||||||||| |||  | || ||  |||| || |     |||  |  || ||      |  | | | || ||      ||  |  | |   || |  ||||      |   |||  |||| ||| |||   | |  
TCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGATTgtacgttctaatgtctatctttatttttgggactgtttgttttttaaataccatacaggtccatgtgatttttttttcaagtcaaattattgttggctggtccactgagtgttatgacctgttaacag-

upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 6
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttactgcctgcctttttatcatctctgcctccttgt-tctcatatgcccctgattcatcgaggctgaaatcgtgtttt-ttctgtctgttgtgaactgcggaaaag---------------------
||| |||||  |||||||  | |||||||| || || |||||||| |||||||||||  | ||||| || ||||| || ||||||||  || ||||||||||| |||      | |  | ||    | |  | ||  |||| | | | || |    |||||||      |    || ||||   || |   |||||| | |||    |  |                     
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaataca---gattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacag

upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G19550.2 (Glycine max), 5'ss of exon 6
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttactgcctgcctttttatcatctctgcctccttgt-tctcatatgcccctgattcatcgaggctgaaatcgtgtttt-ttctgtctgttgtgaactgcggaaaag
||| |||||  |||||||  | |||||||| || || |||||||| |||||||||||  | ||||| || ||||| || ||||||||  || ||||||||||| |||      | |  | ||    | |  | ||  |||| | | | || |    |||||||      |    || ||||   || |   |||||| | |||        
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaataca---gattcatgtgatattttttcatgttcaattattgttgttgtcagctg--------

upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 6
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttactgcctgcctttttatcatc-tctgcctccttgttctcatatgcccctgattcatcgaggctgaaatcgtgttttttctgtctgttgtgaactgcggaaaag
 || || || || |||||  | |||||||| ||||| ||||| || |||||||||||||| || || |||||||| || ||||| ||  || ||||||||||  |||    ||  ||||| | ||||  | ||  |||   || |  | | |     |   |   |  | | |  |    | ||    ||| || | |            
CCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgtgagttg--accatcctttctttcattatatgattccacatt-tagtttacttggaaaaaaaaaaaacaggatgctgaatattatgatcttttctcag-----------

upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgtt-actgcctgcctttttatcatctctgcctccttgttctcatatgcccctgattcatcgaggctg--aaatcgtgtttt-ttctgtctgttgtgaactgcggaaaag
 || || || |  |||||  | |||||||| ||||| ||||| || |||||||||||||| ||||| |||||||| || ||||| ||  || ||||||||||  ||  ||   |   | ||| || |||  ||  |||   || |    | |     |   |   ||| ||   |||  | |  | || | || |                  
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatc--tgattccacatt-tagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag------------------

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|78023452|gb|DV491839.1|DV491839
EST:     TACATCAAGGATGCCATCGAAGCTGTTGTGTTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: TACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|60350531|gb|DN217504.1|DN217504
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|149013843|gb|EE043323.2|EE043323
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|211201981|gb|FL057813.1|FL057813
EST:     GGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|6095362|gb|AW120029.1|AW120029
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGTTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|149048836|gb|EE048336.2|EE048336
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|78088131|gb|DV516524.1|DV516524
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCGGAGGATT                         GAAAATCCTGCTGGAGCCAATGGGTCACATCTTCAATGTTGGGAATCCTGA
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAAT-GGTCACATCTTCAATGTTGGGAATCCTGA
EST: gi|20507862|gb|BQ279797.1|BQ279797
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGTTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|32859492|gb|CD999173.1|CD999173
EST:     GGATGCCATCGAAGCTGTGGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|29130958|gb|CB381662.1|CB381662
EST:     TCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: TCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|89755200|gb|DY685717.1|DY685717
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|148943582|gb|EC888645.2|EC888645
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|60342920|gb|DN209893.1|DN209893
EST:     GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
genomic: GAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGAC
EST: gi|32943135|gb|CF047954.1|CF047954
EST:     TGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCC-GAA
genomic: TGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTG-A

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: 491

TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGACAATGAGGTTACGGTTAGGGAGTTGGCCCAAATGATGACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGACAATGAGGTTACGGTTAGGGAGTTGGCCCAAATGATGACAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 140

TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGACAATGAGGTTACGGTTAGGGAGTTGGCCCAAATGATGACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 721

TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttact ... tgcggaaaagGAAAATCCTGCTCGAGCCAATGGTCACATCTTCAATGTTGGGAATCCTGACAATGAGGTTACGGTTAGGGAGTTGGCCCAAATGATGACAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgttactgcctgcctttttatcatctctgcctccttgttctcatatgcccctgattcatcgaggctgaaatcgtgttttttctgtctgttgtgaactgcggaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT