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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag

Basic information

species Selaginella moellendorffii
transcript EFJ20301
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag--------------------------------
 |  | || ||| | || |||||||||  ||| || || |||||| |||| ||||||||||||||||| ||||||||  |  | ||||| || ||||||||||   |            | |||||  ||| |   || |  |||   | || ||| |||    ||  |                                   
CGCCTCGTCAACCTCATCGGATGCTGCGCCGAGGGCGACGAGAGGCTGCTCGTCGCCGAGTACATGCCCAACGACACCCTTTCCAAGCATCTCTTCCACTgtactctactaccataccctcttcct--cttcatttcgcc--atttccgtatccatgtccactactaggagtaactacttgggtgacgtacttggtgatgatcc

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaag------------attgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag----------------
 |  | || ||| | ||||| ||||||  ||| ||||| |||||| |||| ||||||||||||||||| ||||||||  || | ||||| || |||||||||| |              |  || |  |        |  || | | |    |   ||  |   |    |  |    ||| | |                
CGCCTCGTCAACCTCATTGGCTGCTGCGCCGAGGGTGACGAGAGGCTGCTTGTCGCCGAGTACATGCCCAACGACACCCTGTCCAAGCATCTCTTCCACTgtacgtgctctccacctgctagggatactccagcatttttctgttatatacgggcctcgcgggctggagttgtgtcgtctacggctacggtgaccgtggg

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgcgg------gtggtttttttcctgactt------taaaacggc--gaattcatgcattcatttccttctctctgcag--------------
 |  | || ||| | ||||| ||||||  ||| ||||| |||||| |||| ||||| ||||||||||| ||||||||  || | ||||| || |||||||||| |    |||        || | |   || | | |      |  | | ||  | | |  | ||  | ||| ||    |||   |              
CGCCTCGTCAACCTCATTGGCTGCTGCGCCGAGGGTGACGAGAGGCTGCTCGTCGCTGAGTACATGCCCAACGACACCCTGTCGAAGCATCTCTTCCACTgtacgtgctcggtgctctccgggtctcccccagtccttccctatccacctgccaggactactccagcctttttctgtcgtctatggtgacgtactcgatg

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattg-cgggtggtttttttcctgact-ttaaaacggcgaattcatgcattcatttccttctctctgcag--------------------------
 |  |||  ||  |||| || ||||||| |||  | |  ||| |  | || |||||||||| ||||||| |||| || ||| ||||||| ||||||||||||| | |||     |  ||  |||||   || ||  |   ||     |  |||    |   ||| |    |  |                          
CGGCTGGCCAATCTGATCGGTTGCTGCTACGAGAGCGGCGAGCGTCTCCTCGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttggtttctccttcctttcccctctcttgcattagctgcaactagcacatctgggcttgttagagttgattctgatttggtagtgtactagttc

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv18s0001g00180.t01 (Vitis vinifera), 5'ss of exon 2
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaag----attgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag------------------------
||| | |  || |||||||| | ||||||||| |||||||||||| |||| || || ||||| ||||||||||| ||  |  | ||||| || |||||||||| |     ||  || ||  ||| ||  |||   |  |        ||      || ||| |    | | ||                           
AGACTTGCGAATTTGATTGGGTACTGCTGCGATGGTGATGAGAGGCTGCTTGTGGCTGAGTATATGCCGAACGATACTCTTGCGAAGCATCTATTCCACTgtatgtgctgtttgggttgaatttgtttttgataatgcatttattggtttgaatgttgattgctccttgtttggttgccgagaaactgaggaaaagtaaa

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv08s0007g01520.t01 (Vitis vinifera), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag----------------------------
||||| |  || ||||||||||| ||||| |||||||||||||| ||||| || || ||||  ||||| || || ||  |  | ||||| ||||| |||||| ||  |    | | || | |   ||  |||   |     | ||| ||  |  | |   | ||   ||                               
AGATTAGCGAATTTGATTGGATGTTGCTGTGAAGGTGATGAGAGATTGCTCGTGGCAGAGTTTATGCCAAATGAAACTCTTGCGAAGCATCTTTTTCACTgtgagtgtttttgagtttctctatatgtgtttttgaaatttagttcctgtgtggaatgtgtgcttagtgttatgtaaatttttgctgctagtgtgaaaga

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag----------------------------------
||| |||| || |||||||||| |||||| |||||||||||| | ||||| || || ||||| |||||||| |||||  |  | || ||  | || |||||||||  |     | ||  | |    | ||| |  || | |    ||   |||||||| ||||     |  |                                  
AGACTGGTGAATTTGATTGGATACTGCTGTGAAGGTGATGAGCGTTTGCTTGTTGCGGAGTATATGCCGAATGACACTCTTGCGAAACATTTGTTTCACTgtaagtgtcatatttgtcgtgtggaagccttcattacagagg---ca---attcattttcttcgagaggtggtttgtaacctaacttttctgtgagaaatgtgttg

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 5'ss of exon 3
AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgcgggtggtttttttcctgactttaaaacggcgaattcatgcattcatttccttctctctgcag---------------------------------------------------------------------------------------------------------
|||||||| ||||||||||| |||||||  || ||||||||| | || || || || ||||| ||||||||||| || ||| ||||| |  | || ||||||||  ||     |  ||     | ||  |||  |  || |  || || |||    |  ||| |    | ||                                                                                                         
AGATTGGTGAACTTGATTGGCTGCTGCTATGAGGGTGATGAGCGTTTACTTGTTGCGGAGTATATGCCGAACGATACTTTGTCAAAGAATTTGTTTCACTgtaaatttctc--tcattgaacccatgcattttgagtggagggtt-atacataacatctcttgtgcacgaagggaagttgcttttcaatttcttactgttaagtcggagatttgaggtctaccatggtcacactttgcaaagacaatgacagtttgttgatcatcaacattctacag

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|169075974|gb|FE480982.1|FE480982
EST:     AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACT                         GGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
genomic: AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgc ... ctctctgcagGGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
EST: gi|169097974|gb|FE498771.1|FE498771
EST:     AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACT                         GGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
genomic: AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgc ... ctctctgcagGGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
EST: gi|169102668|gb|FE504461.1|FE504461
EST:     AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACT                         GGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
genomic: AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgc ... ctctctgcagGGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
EST: gi|169082053|gb|FE490565.1|FE490565
EST:     AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACT                         GGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA
genomic: AGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgc ... ctctctgcagGGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACA

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 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 42

AGATTGGTTAACTTGATTGGATGCTGCTGCGAAGGTGATGAGAGGTTGCTAGTCGCCGAGTACATGCCGAACGACACATTGACAAAGCACCTTTTCCACTgtaagattgc ... ctctctgcagGGGAAAAGCAACCTATGCAATGGAGCATGCGCCTGAGAGTGGCTCTCTACATTGCACAGGCACTGGAGCATTGCAGCAATAATAACCGTCGTTTATATCA




<











<


<