Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcactattgcataataagtttacatttaccttttgttttgtatctctttatcaacaagagatggtatccattgtcacttttg...

Basic information

species Zea mays
transcript GRMZM2G123624_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcactattgcataataag-tttacat-ttaccttttgttttgtatctctttatcaacaagagatggtatccattgtcact-tttg
 ||||||||  |||| |||||||| ||||||||||||||||| ||||| ||||| || |||||||| |||||||| |||||||| ||||| ||||| ||||| || ||  |||| |    ||| |    || ||   || | || || ||| ||||| ||    | | ||| ||  | | |  || |  |   |   | | ||
GGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCACAGgttatctcactatgaaacatactgtctt-tactacccttcatatgttgcctattgttatggtgatttctattaa--acatactgtctttaccctttttatctg

upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G01120.2 (Glycine max), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcactattgcataataagtttacatttaccttttgtt---ttgtatctc------tttatcaacaagagatggtatccattgtcacttttg-------------------------------------------------------------------
|||||| ||  | ||||| ||||| ||||||||||| |||||||||||||| || || || ||| | || ||||||||||| || ||||| ||||| ||||| || | ||  | ||| |    |||  ||  ||  |||   ||||  | |       ||  || |       | | | ||  ||  |   | ||     | | ||||                                                                    
TGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCCAGgt-atctggaattttatctt-tcattttattgtacttttttttttatttgtcaccagcttacattttgagaaatgtctgaatgagtaactatttcatcaatgatttttttcctttgtactttgtaattacactgtcttttaaacctagacaggctattgaagtttccaaacgccag

upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G01100.2 (Glycine max), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatat----gtatttcactattgcataataagtttacattt------accttttgttttgtatctcttt-atcaacaagagatggtatccattgtcacttttg---------------------------
|||||| ||  ||||||| ||||| ||||||||||| |||||||||||||| || || || ||| | || ||||||||||| || ||||| ||||| |||||   |   || |    ||| ||   |  |   | |   | ||||||||      |  | |   |  |||||| ||| |||||| |    |  | |||  |||   ||||                            
TGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCACAGgtatctggaattttattgtacttttttcatttgtcacctgcttacattttgggaaatgtctgaatgagtatctgtttcatcaacgatttttt-tttcctatgtactttttaattacactgtcttttaaacctagacag

upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G04210.1 (Glycine max), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga-tatgtatttcacta----ttgcataataagtttacatttaccttttgttttgtatctctttatcaacaagagatggtatc-cattgtcacttttg-----------------------------------------------------------
|||||| ||| | || || |||||  |||||||||| ||||||||||| || || || || ||| | || ||||||||||| || ||||||||||| |||||| | | || | | | ||||| |     || || ||   |||     |    |||  |||   | ||  || |   |        || |  || ||    |||                                                             
TGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCCAGgtgttctagaatttatctttcatttaacttttcaaaacttgttggacatcctttttcatttgtcacctgctttttgtctgtcttctgtgtttcagtgcatgtttcattaatgattttattttattattttgttgtgtaattactctgtcttttgaacctagatag

upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G01120.1 (Glycine max), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcactattgcataataagtttacatttaccttttgtt---ttgtatctc------tttatcaacaagagatggtatccattgtcacttttg-------------------------------------------
|||||| ||  | ||||| ||||| ||||||||||| |||||||||||||| || || || ||| | || ||||||||||| || ||||| ||||| ||||| || | ||  | ||| |    |||  ||  ||  |||   ||||  | |       ||  || |       | | | ||  ||  |   | ||     | | ||||                                            
TGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCCAGgt-atctggaattttatctt-tcattttattgtacttttttttttatttgtcaccagcttacattttgagaaatgtctgaatgagtaactatttcatcaatgatttttttcctttgtactttgtaattacactgtcttttaaacctagacag

upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcacta--ttgcataataagtttacatttaccttttgttttgtatctctttatcaacaagagatggtatccattgtcacttttg----------------------------------
||| || ||| |  | || |||||| |||||||||| |||||||||||  | || || || ||| | || ||||||||||| |||||||||||||| |||||    |  |     ||  ||  |   |   |||| |   |   |  |   |  ||||| |     |  |  ||| ||  ||  |||  |||  ||   | |                                  
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttatt-attcgcatgatagaactttacttatgcgcctgctttaatccaaacag

upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 5'ss of exon 5
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgat--atgtatttcactattgcataataagtttacatttaccttttgttttgtatc-tctttatcaacaagagatggtatccattgtcacttttg
|||||| ||| | ||||| ||||| ||||||||||| ||||||||||| || || || || ||| | || || |||||||| |||||||||||||| |||||  | |  |   || |  || | | || || |||   |  || |||  | |  | ||||  || | |||   |        |  |    | | |   |||  
TGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTCAGgtattcttaaacaattttatttagtttttca-aatgtatgcacttttctcctagggtttgagtcatatttgatattttcttttattgctgagtttttgttt--

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|19822322|gb|BQ048346.1|BQ048346
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAATCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|76935690|gb|DV174431.1|DV174431
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|149085095|gb|EE174602.2|EE174602
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|71765024|gb|DR962961.1|DR962961
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|71768414|gb|DR966351.1|DR966351
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|71434707|gb|DR815757.1|DR815757
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|211244356|gb|FL352760.1|FL352760
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|20506722|gb|BQ279315.1|BQ279315
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAATCTGAAGCGCAG                         GCTATTGAAGCTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|71328410|gb|DR800842.1|DR800842
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|74244904|gb|DT652818.1|DT652818
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|74239024|gb|DT646938.1|DT646938
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
EST: gi|71328409|gb|DR800841.1|DR800841
EST:     CCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT
genomic: CCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 192

TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAATAGTGATATGATTTCAAGGCTAGAAGCGGCTGAGTCAAAGCTGCAGGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAATAGTGATATGATTTCAAGGCTAGAAGCGGCTGAGTCAAAGCTGCAGGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAATAGTGATATGATTTCAAGGCTAGAAGCGGCTGAGTCAAAGCTGCAGGAGT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 115

TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcga ... agtcctgcagGCTATTGAAGTTTCAAAACGCCAAATGAAACTAAGAGAAGCATCTGGAAATAGTGATATGATTTCAAGGCTAGAAGCGGCTGAGTCAAAGCTGCAGGAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcactattgcataataagtttacatttaccttttgttttgtatctctttatcaacaagagatggtatccattgtcacttttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaagag