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

GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag

Basic information

species Selaginella moellendorffii
transcript EFJ27053
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttt--tcttttctccaccttagctaggatcttctcttgttttctccatg-catgctactttctaactagaacttgtgatttctcag
|   ||    ||  | | | |   |   || || ||||| ||  ||||||||||  |||||||||||||||||||||||||||||||||| ||||||||||    |   |||    |||  ||  ||  |  |   |  | ||      | | |      | | |   |   | ||   |  ||  || |||||||      
GGCGGAGGAGGGTGGAGGGCTCGCGAAGACGCTGCAGCTCGGCGCGCTCTTCGGGCTGTGGTACCTCTTCAACATCTACTTCAACATCTACAACAAGCAGgtgaggcggctttaactttgatccattgccgtcgccaatttggcggagatttgggggagactaggatgtttcatttgggatttattacatgtgattctgt--

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgc-attgtttcttctcgttttcttttctccaccttagctaggatctt---ctcttgttttctccatgcatgc-tactttctaactagaacttgtgatttctcag
| | ||    |  ||||   |       || || ||||| ||  |||| |||||  |||||||||||||||||||||||||||||||||| ||||||||||  |     |   ||  |  |||          | |    | ||        || |  | ||   |   ||  ||  |||  |  |||  ||   ||||| || 
GGAGGAGGAGGAAAGCGGCCTCGCCAAGACGCTGCAGCTCGGCGCGCTGTTCGGGCTGTGGTACCTCTTCAACATCTACTTCAACATCTACAACAAGCAGgtgagcaagtgagcttatgatctggctcttgagtaattgtgaattaaaaatgctggaatgctttgtaattgtgtagattcggatcagagttt---atttcaca-

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g07730.1 (Oryza sativa), 5'ss of exon 1
---GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag
   ||  ||     |  ||||  |   |   ||    ||||||||  |  |  |||    |||||||||| |||||||||||||||||||||| ||||||||||  ||  | |  |          ||||||  | |         | ||||||        ||  ||||     |   |                      
TGGGCGGGAG---AGAGGCGCACTCGCGGAGACGGCGCAGCTGGGCGCCATGATCGTGGCGTGGTACCTCCTCAACATCTACTTCAACATCTACAACAAGCAGgtcttcctcccccctcaagaaccttctccttcctcatcctcgccatctcttaacccaatcagccatggagaatctcag---------------------

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g07870.1 (Oryza sativa), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgc----------attgtttcttctcgttt-------tcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag
    |    || | |||  ||   ||| ||  | ||||| ||  |  |  ||    | ||||||||| |||||||||||||||||||||  ||||||| ||           ||| |||   | |  ||       |   ||||||  ||   |  |    || || | | |  |   | ||||     |  |   | |||    ||  ||  |||
CGGCGCCGTCGCCGGCGGCATTTCGCGGACGGTGCAGCTCGGCGCCATGATCCTCGTCTGGTACCTCCTCAACATCTACTTCAACATCTTCAACAAGCTGgtctgcacatatatttttttcccccaattcgtcaatttccttctccttctcgacatgttctttttcgtctctaatttgttcatggcggatcttg-ttggaatccatggcttg-cag

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag-
  | ||| | ||  | | | |  |    || || |||||||| |||||||||||  | |||||||||||||||||||||||||||||||| ||||||||||     |  ||        ||  |       |   |      | || |         | ||| | || | |      |    || |  ||   || |   
AGAGGAAGCGGGGGGAGGGCTCGTCAAGACGCTGCAGCTGGGGTCGCTCTTCGGGCTCTGGTACCTCTTCAACATCTACTTCAACATCTACAACAAGCAGgtgaactgactgacgaaaatcactggcgtctccctgtccctgtgttgtgcgacgcgttgcattcctgatgcgcgagcaacccaattgctggcctcacctc

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctc-caccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag--
|   |||   ||  ||| | | |||   || ||   ||| || |||||||||||  | |||||||| ||||||||||||||||||||||||||||||||||    || || |  |||    ||   |  ||         |||| |  | || || | |  ||      ||  |  | | ||||  || |  |      |  
GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtga-gtatcctgacgtgagattgggtgacagagcgttcgggatatgttttttttgtgtgtatctgaa-tatctgattattagattttatcttgagatggta

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G047404_T02 (Zea mays), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgattt--ctcag-
  | ||| | ||  | | | |       || || ||||||||  |||| |||||  | |||||||||||||||||||||||||||||||| ||||||||||    | |   |  ||         | |     |  ||    | | |   |||| | |   ||  || | |      |||||   ||  | | |    ||  
AGAGGAAGCTGGGGGAGGGCTCGCCAAGACGCTGCAGCTGGGGGCGCTTTTCGGGCTCTGGTACCTCTTCAACATCTACTTCAACATCTACAACAAGCAGgtga-gctgactgacgggaaaaaaacactgatgtctctccc-tgtccctctgttgtgtgtgtgtgtgatgcgcgggcactagtgattcggttctgatccact

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G008642_T01 (Zea mays), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGg--cattgtttcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag
||| ||   || |  ||  ||   ||  || || || || ||  |  |  ||    | ||||||||| |||||||||||||||||||||| ||||||| ||  |   ||||| ||  |||  |          | ||    || |   |       |      | |    ||  ||||  | | || |     ||   |||
GCAGGAGGGCGCCGCCGGCATTTCGCAGACCCTGCAACTCGGGACAATGATCCTCGTCTGGTACCTCCTCAACATCTACTTCAACATCTACAACAAGCTGgtccgccgtttcgtcctgttccccaagtcttttcgtaatggggttgcgcaaccaaatgggatcttctaattaaattctttcgaaaattgcgagttgggcag

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G066413_T01 (Zea mays), 5'ss of exon 1
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttct----tttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactag-aacttgtgatttctcag
|     |  |||| | |  ||   |  |||    ||||||||  |  |  |||    |||||||||  |||||||||||||||||||||| ||||||||||  | |        ||||  |       |||| |      ||  ||||  |||   | ||||||   | || |  |    | | |    | |      |  |||
GACGACAGACGGCGGTGGCATTGCGGCCACGGCGCAGCTGGGCGCCATGATCGTCGCGTGGTACCTGCTCAACATCTACTTCAACATCTACAACAAGCAGgtctggccggcggccgttcaccgcagcatctcaagagatcctcagatcccctccactcttctccccccctgatgatcaacaccaaccgtcgtcccccgttgcag

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA04G35730.1 (Glycine max), 5'ss of exon 1
-GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtt--tcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag-
 ||     || |  | | || |  |    || ||| | || ||  |  | || ||  | |||||||||||||||||||||||||||||||| ||||| ||||      |  |||    | | |||  |       || ||    |  | || ||      |   ||| |||  | |  | | |  | |         ||  | 
TGCGCCCGTC-GAAAACCCGCTCTTCAAAACTCTCGAACTCGGCGCCTTGTTTGGCCTCTGGTACCTCTTCAACATCTACTTCAACATCTACAACAAACAGgtccgaatactctctcagatctctcgttctagtttttgcctcaacttgcttttaaacgattgttgc-tgcaccataatgattt-accaaacacgcccttgga

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA06G19250.1 (Glycine max), 5'ss of exon 1
-GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgct-actttctaactagaacttgtgatttctcag-
 |||    || |  | | || |  |    || ||| | || ||  |  | || || || |||||||||||||||||||||||||||||||| ||||| ||||   |  |||| | || | |||  ||   | ||||  ||| | |   |            | |  |  |  ||     || |  | ||    || |  |  
AGCACCCGTC-GAAAACCCGCTCTTCAAAACTCTCGAACTCGGCGCCTTGTTTGGCTTATGGTACCTCTTCAACATCTACTTCAACATCTACAACAAACAGgtcctaattctccccgctctctcatcag-atcttatttagaaacaaatgagaaaaaaaaaacgattatttgctgaacgacgatcattttattttacctaac

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv17s0000g08560.t01 (Vitis vinifera), 5'ss of exon 1
--GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttctt--ctcgttttcttttctccaccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag
  || ||||  |||        || | |  ||  | ||||| || | | | |||||  | |||||||| ||||| ||||||||||| ||||| ||||||||||  |  |||  |     || ||||    |      |   | | | |    | | |  |   |   | |  |||   |    |||   |  |   |  | ||
GAGCGAGAAGTCGGGGAACT--TGGTTCAGACGTTGCAGCTCGGGTTGTTGTTCGGTCTTTGGTACCTTTTCAATATCTACTTCAATATCTACAACAAGCAGgtttgtttttgtggtgtgtgttctgaaatttgagatttttcgtagcaaagcctctgatgaactgacgtaataccgccatgttaggcttaattgatg-tgag

upper sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: EDP02676 (Chlamydomonas reinhardtii), 5'ss of exon 2
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgt-tttcttttctccaccttagc-taggatcttctcttgttttc-tccatgcatgctactttctaactagaacttgtgatttctcag-------------------------------------------
|||  |  |   ||  | ||||||||  ||  |   |||||| ||  | ||||     ||||||     |||||||  ||||||||||||||||||||||| | |    |  | |   |  |   || | | |  ||| |   | |  ||||      |  |||     ||  |   | | || |||  |     |   |||                                           
GCAGCAGCC--ACACGGAGATGATGCAGACGTTGGTGCTGGGCTCCATGTTCGCGGGCTGGTACGCAGCCAACATCGCCTTCAACATCTATAACAAGCAGgtacttgcccgacccacatcacaactcacaagcccagcctcccaacccctctcacacacgcccaccggggcccccggccacctggaaaatccacctcagcaggctttaaccaaccctctatttctgtttccttgcacttgcacag

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|169106063|gb|FE506165.1|FE506165
EST:     TCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTGCTCAAGGTCTTTCCATTTCCGATCACGATCACTGAGATCCAATTCGCC
genomic: TCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttc ... gatttctcagGTGCTCAAGGTCTTTCCATTTCCGATCACGATCACTGAGATCCAATTCGCC




















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: 34 (upstream exon), 35 (downstream exon)
Score: 5

GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttc ... gatttctcagGTGCTCAAGGTCTTTCCATTTCCGATCACGATCACTGAGATCCAATTCGCCATTGGGTCCGCTGCCGTGCTCTTCATGTGGACTACGGGACTGTACAAGC




<











<


<