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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtatatattacttgtccttctatggaagatgggcattatggacctgactgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA

Basic information

species Zea mays
transcript GRMZM2G036034_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 14
gttggtatatattacttgtccttctatggaagatgggcattatggacctgactgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
       |    |   ||| ||| |||          |   |   |  | |||   |   |     | |||| | ||||||| | |    || |||||||| || |||||||||||||| |||||||| |||||||| ||||| |||||||||||||| |||| ||| || |||||||||||||||||||| ||||
------gttagcttggtgttcttttattttgttcccactgaaaatatatcactatgttctaccacttatgttttgactttttatcctttttttcagTCATCAGCTCCTGTAGAATTGACCGAAGCTGAAACTGAATATTCAGTCAATGTTGTGAAGCACATTTATGACGGGCATGTTGTGCTCCAATACAATTGTA

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 14
gttggtatatattacttg-tccttctatggaagatgggcattatggacctgactgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
    || | | | ||||| | || ||  |  |       ||| |  |  | |   | |    ||  || | |   |  | ||| ||     | |||||| || |||||||| ||  | |||||||||||||| |||||  ||||||||||  | || || ||||||||| | ||||||||| |||| |||||||| |
----gt-tctttcacttgattctgctccgaca-------attctatattttatgtagttcttttctatatctaaaatgtattttttt---ttaccagTCCTCAGCACCTGTGGAGCTCACTGAAGCTGAGACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 14
gttggtatatattacttgtccttctatggaagatgggcattatggacctgactgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
|||  |  |  ||  || | || | |   |   |     ||||| |  |   |   |   || | ||||| | |   ||||  |      | |||||| || ||||| || ||  | |||||||||||||| |||||  | ||||||||  | || || ||||||||| | ||||||||| |||| |||||||| |
gttctttcac-ttgtttctgctcccaca-attctatattttatgtagttctttctgt---atctaatgtggtatgtattttgatattttttaccagTCCTCAGCACCCGTGGAGCTCACTGAAGCTGAGACAGAATATGCTGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA11G12610.1 (Glycine max), 3'ss of exon 14
gttggt--atatattacttgtcc-----ttctatggaagatgggcattatggacctg-actgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
|||  |  |   | | |||||       ||||||     ||      | |  |  |  ||||||     | | |||| ||   |  | ||| |     | |||||| || | |||||| ||  | |||||||| ||||| |||||  ||||||||||||| || || ||||||||| | ||||||||| | ||||||||||| |
gttatttgactcaattcttgtttcataattctataatttatatcttctttccatatatactgaaatatgtattatgtattccga--tgttgcttttcttaccagTCTTCAGAACCTGTGGAGCTTACTGAAGCAGAGACAGAATATGCAGTTAATGTTGTTAAACACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 14
gttggtatatattacttgtccttctatggaagatgggcattatggacctgactga-atctcatttgatgtgttgtaactttttgt-tcgcacttc---cagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
|||  | ||  |   |  |  ||| |    | ||      |||   | |  || | ||    |   ||||  | |   || |  | | ||  |     ||||| || | |||||| ||  | |||||||| ||||| |||||  ||||||||||||| ||||| ||||||||| | ||||||||| | ||||||||||| |
gttattttacttagttcttgtttcaaaattatatactttatattttctttccttatatactgtaatatgtactatgtattctgatgttgctttcttatcagTCTTCAGAACCTGTGGAGCTTACTGAAGCGGAGACAGAATATGCAGTTAATGTTGTTAAGCACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 14
gttggtatatattacttgtccttctatggaagatgggcattatggacctgactgaa----tctcatttgatgtgttgtaactttttgttcgcactt-ccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
       |    | ||| |  |   ||         |||  ||||||     ||||    |   | || |   ||| |   |||||  |   | ||  ||||| || |||||||||||  |||| ||||| || || |||||  | ||||||||||| ||||| ||||||||| | ||||||||| |||| |||||||| |
------gtcccctgctttttttcacatacgcttcatgcac-atggactaatttgaaatgttactaattcagaagttattcttttttcgttttatttatcagTCCTCAGCACCTGTAGAGCTGACAGAAGCAGAAACAGAATATGCTGTTAATGTTGTCAAGCACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

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|211006550|gb|FL418097.1|FL418097
EST:     AGCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAG                         TCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAAT
genomic: AGCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAGgttggtatat ... gcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAAT
EST: gi|211376755|gb|FL398876.1|FL398876
EST:     AGCT-CTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTA-G                         TCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAAT
genomic: -GCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAGgttggtatat ... gcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAAT

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), 47 (downstream exon)
Score: 275

GGCATCTGCTGTCAGTGACCCTGTTTCTACAGTTGATGCTTCGTATGAGAAGCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAGgttggtatat ... gcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GGCATCTGCTGTCAGTGACCCTGTTTCTACAGTTGATGCTTCGTATGAGAAGCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAGgttggtatat ... gcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

GGCATCTGCTGTCAGTGACCCTGTTTCTACAGTTGATGCTTCGTATGAGAAGCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAGgttggtatat ... gcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 364

GGCATCTGCTGTCAGTGACCCTGTTTCTACAGTTGATGCTTCGTATGAGAAGCTTCTTTCGTCCATTCCCGAATTCGCTGATTTTGGAAAGCTTTTTAAGgttggtatat ... gcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggacctgactgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA
                             ttgtaac  putative branch site (score: 364)
                                              cacttcc  putative PPT
                                taacttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtatatattacttgtccttctatggaagatgggcattatggacctgactgaatctcatttgatgtgttgtaactttttgttcgcacttccagTCATCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA