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

gttggtgactattggtttctactatgtggtttggcaaataatgtggaatgtggaaatgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA

Basic information

species Zea mays
transcript GRMZM2G178618_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 4
gttggtgactattggtttctactatgtggtttggcaaataatgtggaatgtggaaatgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
|||||||| | ||| ||  |||| ||  |||      |   | ||||   | ||||         | |||| |   || | || |||| ||||| || || ||||| ||||||||||||||||||||||| ||||||||||| || || ||||| || ||||||||||| || || ||||||||||
gttggtgaatgttgattgttactttgcagttctctgcagtctatggatctttgaaag------tgtctgtgttacatttgttgcagGTTATCATCGTGACCAGCTCGTTGATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCTAATGCAATAAGAGTTCTTTGCCGCATCATTGACTCAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
---------gttggtgacta-ttggtttctactatgtggtttggcaa--ataatgtggaatgtggaaatgactttcatttgtgatctgttgggt--gtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
           |  |||| | |  | |||    || |||| ||   |  | ||   |  ||   ||     || ||  || |  | |  |   |    |||| ||||| || ||||||||| | ||||||||||||||||| || |||||||||||| | || ||||||||| | || ||||||||||| |  ||   ||
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 4
-----------gttggtgactattggtttctactatgtggtttggcaaataatgtggaatgtggaaatgactttcatt-------tgtgatctgttgggt------gtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
            |  |  ||| ||  ||| |  ||| |  ||  | |     ||||   ||||  | | ||||  |||       |   |||| ||   |       ||||| ||||| || ||||||||| | |||||||||||||| ||||| | |||||||||||| |||||||| ||| |||| || |||||||| | ||||  ||
gtttcattttcttatgcaacttttattttattttatattcttgtgtatggtctgtgatctgtgttactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGACATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 4
------------------gttggtgacta-ttggtttctactatgtggtttggcaa--ataatgtggaatgtggaaatgactttcatttgtgatctgttgggtg--tagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
                   ||  |||  | |  | |||    || | || ||   |  | ||   |  ||   ||     || ||  || |  | |  |   |    |||| ||||| || ||||||||| | ||||||||||||||||| || |||||||||||| | || ||||||||| | || ||||||||||| |  ||   ||
gttacaaattcttgcaattttcatgagcagtcagattcacgaatattgtctgtatatcacaaacagagattctgaccgttctatctcttttattttacttttttaccagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACGGATGGAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 4
-----------------------------gttggtgactattggtttctactatgtggt-ttggcaaataatgtggaatgtggaaatgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
                              ||   || |  ||   | |  |||||| | ||    | |||  |||| | |  ||||    |   | | | || | |      ||||| ||||| || ||||||||| | |||||||| ||||| ||||| | |||||||||||| |||||||| ||| |||| || |||||||| | ||||  ||
gtttcattttcttatgcaacttttcttttattttagattcatg-cgtatggtatgtgatctttattactaacttggattat--aaatattctatctctttaattttt---aaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGATATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
gttggtgactattggt---ttctactatgtggtttggcaaataatgtggaatgtggaaatgactttcatttgt--gatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
||  || | | ||  |   ||  | || |    | | |  |   | | | | ||  |  |     | | ||||  | | | | |    ||||| ||||| |||||||||||| |||||||||| |||||||| |||| ||||||||| || |||||||||||  | || || || || || || |||  ||
gtctgtaaattttactcaatttcaatacgaacatcgtcgcact-tattgtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
gttgg--tgactattggtttctactatgtggtttggcaaataatgtggaatgtggaaatgact--ttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
|||    ||| | |||  || || |   | |||||   |  ||  |    |||| |||   ||   |  ||| | || | |       |||| || || || || |||||  | |||||||||||||||||||| ||||||||||| || |||||||||||| | ||||| ||||| || |  ||   ||
gttaaattgattgttg--ttttatttgtttgtttgt--accaactttatttgtgaaaagtgctgactggtttataatttatatacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------gttggtgactattggtttctactatgtggtttggcaaataatgtggaatgtggaa-atgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
               || |  || ||  ||        ||    ||     || |    ||| || ||  |  |  || |            ||  |  |||| ||||| || |||||||||||||||||||| ||||| ||||| || ||  | || ||||||||||| || || ||||| ||||| || |  |||    
agcttgacatagagattagatacgatatgtgaaggtc-tgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S15_298V6.2 (Physcomitrella patens), 3'ss of exon 3
------gttggtgactattggtttc-tactat---gtggtttggc-aaataatgtggaatgtgg----aaatgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
         |||  ||   |||||  ||   |   |  ||   |  ||||  | |    |||||      | | | || | || | |   ||  |  | |||| ||||| |||||||| ||||| |||||||||||||| ||||| || ||  | || || || ||||| || || || || ||  | || |  |||    
aatacttccggtctcttaaggttttatatggtagaggagtacagtgaaatcgttttagttgtggttaggtacggcattgacttat-acaagtctgtggcagGTAATCATTGTAACAAGTTCTTTAATGAAGGACATGAACAGCAAGACAGACCTCTATCGCGCGAATGCCATAAGGGTGCTGTGCAGAATCACGGACGGTG

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|18655281|gb|BM500086.1|BM500086
EST:     GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAG                         GTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
genomic: GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
EST: gi|148956209|gb|EC901999.2|EC901999
EST:     GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAG                         GTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
genomic: GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
EST: gi|22490147|gb|BU050070.1|BU050070
EST:     GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAG                         GTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
genomic: GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
EST: gi|148931355|gb|EC874250.2|EC874250
EST:     GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAG                         GTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
genomic: GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
EST: gi|87153597|gb|DY398386.1|DY398386
EST:     GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAG                         GTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
genomic: GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
EST: gi|74235981|gb|DT643895.1|DT643895
EST:     GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAG                         GTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT
genomic: GGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGAT

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: 249

GGTCTTCTTTGCAACGACCAAGCTGTTCCAGTCTAAAGATGCGGGCCTTAGGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 218

GGTCTTCTTTGCAACGACCAAGCTGTTCCAGTCTAAAGATGCGGGCCTTAGGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

GGTCTTCTTTGCAACGACCAAGCTGTTCCAGTCTAAAGATGCGGGCCTTAGGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

GGTCTTCTTTGCAACGACCAAGCTGTTCCAGTCTAAAGATGCGGGCCTTAGGAGGATGGTGTACCTCATGATCAAGGAACTCTCACCTTCAGCCGATGAGgttggtgact ... ttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaaataatgtggaatgtggaaatgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA
     aataatgt  TA-rich tract