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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaattcattcttgtcatttgaagcatgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC

Basic information

species Zea mays
transcript GRMZM2G139977_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 9
gtaagaattcattcttgtcatttgaagcatgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
||||||| | | ||  ||  | |     | |||    | |||   |   ||   |  | |   || ||| || | ||||| ||||||| | |||||||| || ||||||||||||||||||||||| ||||| || |||||||||||||||||||||||||||||||| |||||||| | ||||||||||||||
gtaagaaattagtccagtattctttcaaaagaacaccaatcatttcaagcataaatca-tacgtgaaactgttt-tttatcaaatgtttggcagGCTGTCCTTTTGTTCCAGAAAATAGAAGGTGTAGAAGTGTGCCTATTTGGAATGTATGTTCAAGAATTTGGTGCAGAATGCTCCTACCCGAACCAGCGTC

upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 11
---gtaagaattcattcttgtcatttgaagcatgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
    | ||||       || ||| |   | | | ||| | | |||  | |||    || || ||  |||  || ||  |||      | ||   ||||  ||| | ||||| || || ||||||||||||||||| || |||||||| ||||||||||||||||||||  |||||||    || || || ||||| |
gtgatgagaaagttgatttatcaatctgatcgt-aatcg-aatcattaatcatgaatattatttgatgc--ccttagctttc-----tatt--ccagGTAGTTTTGTTGTTTCAAAAGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 9
gtaagaattcattcttgtcatttgaagcatgaattgtagtca-caactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
||||      |   ||| | || ||   |   ||  | || | ||| ||     || | |||   |     |   | || ||   |      ||||   |  | ||||| ||||| || ||||||||||||||||| || ||||| |||||||||||||| |||||  |||||||    || ||||| || || |
gtaaagg--gaaggttg-ctttagagctagtcatgttggtaatcaagtcgttattatttattctggattttgatgacttttggtttccatttcagGTAATCTTGTTGTTTCAGAAGATTGAAGGTGTGGAAGTATGCCTCTTTGGCATGTATGTTCAAGAGTTTGGATCTGAATGTCAATTTCCGAATCAACGGC

upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 9
-----gtaagaattcattcttgtcatttgaagcatgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
     |  | | || ||| |   |||  ||    || | |  | |||  | |||    ||||   ||      || ||  |||      | ||   ||||  ||| | ||||| || |  ||||||||||||||||| || |||||||| ||||||||||||||||||||  |||||||    || || || ||||| |
gtgatgggaaagttgattttatccatccgat---tgtaatcaaatcattaatcatgaatact---tttgattcccttagctttc-----tatt--ccagGTAGTTTTGTTGTTTCAAAGGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------gtaagaattcattcttgtcatttgaag----catgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
               | |     ||||| |  |   || | |    |||  | | |  |||  | ||     |  || |     |   |||   |  |     | ||   ||||  |||||  |||||||||| ||||||||||| ||||||||  | ||||| |||||||| |||||||||||  | ||||| ||    || || || || |
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgc-tccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC

upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaattcattcttgtcatttgaagcatgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
    | || ||   |    |||      |||  || |  | | |  | |||   ||| |  |    ||| | | |||       |  |   ||||   || | ||||| ||||| || ||||| || ||||||||  ||||||| ||||||||||||||||||||  | |||||    ||||| || || ||||
----gtatgcaggatgtatattaagttgatgttttttcat-atagttgacaaagacttaaattatgaactgaagattgtctttttcgtttccagGTAATTTTGTTGTTTCAGAAGATTGAAGGAGTAGAAGTATGCTTATTTGGGATGTATGTTCAAGAATTTGGATCAGAATGTCTATTCCCAAATCAACGTC

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: 103

AGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 67

AGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

AGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 87

AGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC
              tactaat  putative branch site (score: 87)
                                tatatttatgaaatgt  TA-rich tract