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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag

Basic information

species Selaginella moellendorffii
transcript EFJ10353
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 5'ss of exon 4
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag----
 ||| |||| ||||| |||||||||||||||||||| ||||| || ||||||||  |||| || ||||||||||| ||||| ||||||||||| |||||||||       ||        ||    |  |    || ||     | ||||     || |  |   ||    |   |    
-GCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACAACATATATGGCCCCTTTGGAACATGGAAAGgtagaagtttaaccaattctccaagttattgaactgtacttgtactggggcatccttaactcaatttgtcaatggatag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 5'ss of exon 3
TGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgcttctttagcctga--gtgggagtaactgagattgtttcaaaac-cag
   ||||| || ||||||||||| ||||| ||||||||||| || || || ||  |||| || || || || |||||||| ||||||||||| ||||| ||| || | | | ||   |  | |  |    |||   ||   | |  || | ||| |     |||| ||       |||
GCTACTGAGGAACTGTGCAAGCATTACACAAAGGATTTTGGCATTGAATGTCGGGTTGGCCGCTTTCATAATATCTATGGTCCCTTTGGAACATGGAAGGgtaagct-acatatctggtacctagtaaaacttgggtattgttactgtagaagttataataattgattggctctacag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 5'ss of exon 4
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag----------------
 ||| | || |||||||||||||||||||||||||| ||||| |||||||||||| | || || |||||||||||||| || || || ||||| |||||||||||    |      |   |||      ||  | |   | |    |   | |      |  || |  ||||                    
-GCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACAACATCTACGGCCCTTTCGGAACATGGAAAGgtgaacctactaccagttttctgggctgtggctgtgaggtc---ataacaatccaacggcctgataaaaaaatgctctctttgtctatcag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G138907_T01 (Zea mays), 5'ss of exon 4
TGC-ACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag---------------------------
 || ||||| ||||||||||||||||| || ||||||||||| ||||||||||| ||||| || || |||||||| ||||| ||||| || || ||||||||| ||||       ||  | ||  |  |   ||       ||  || || |  |  ||  || |     |    |                           
-GCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgctatctggtagctagtagtattttgccagttctttgttggtgctatcgattttctagatgacgttgtcctatgtttattgcttggcaatatag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 3
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcat----agattgagatcttcttcttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag-------------------------------------------------
 ||| | || ||  | ||||||||||| | |||||||||||| || ||||||||||||||  | ||||||||||| || || || ||||| || ||||||||   |||  |      ||||| | ||| |      ||   |   |  | ||||   |   |   |  ||| | |    |                                                 
-GCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACAACATATACGGTCCTTTTGGGACATGGAAAGgcatgtttttcactgaattgaaagcttttatagttttgactttaccaaatgggtaaattggtagtcattttatattttggtaacctttcggatttaataagtttgtgttttgttgttttgtcatacag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA20G36740.2 (Glycine max), 5'ss of exon 4
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttca----tagattgagatcttcttcttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag-------------------------------------------------
 ||| | || ||  | ||||||||||| | |||||||||||| || ||||||||||||||  | ||||||||||| || || || ||||| || ||||||||   | |      |  ||||| | ||| |      || | |   |  | ||||   |   |      ||| |      |                                                 
-GCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACAACATATACGGTCCTTTTGGGACATGGAAAGgcatgctttacactgaattgaaaacttttatagttttgtctttaccaaatgggtaaattggtagacattttatgttttggtaaccttttggatttaataagtttgtgttttgttgttttgtcatacag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 4
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgc--ttctttagcctgagtgggagtaactgag---attgtttcaaaaccag-----------------------------------------
 ||| | |||||| | |||||||| || | |||||||||||| || ||||||||||||||  ||||||| ||||| ||||| || | ||| || ||||| |||  |||| |   |  |   |   || ||||  || ||     | |||  |   |  || |   ||| |||   | ||                                           
-GCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGGgtatgttcttgactgcattgcaagtttttgcggttgttgtatttaagtcagtagacttgtgggcattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA19G43400.1 (Glycine max), 5'ss of exon 4
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttcttgc--ttctttagcctgagtggg---agtaactgagattgtttcaaaaccag-----------------------------------------
 ||| | |||||| | |||||||| || | |||||||||||| || |||||||| |||||  ||||||| ||||| ||||| || | ||| || ||||| |||  |||| |   |  |   |   || ||||  || ||     |||||      | ||   || ||| |||   | ||                                           
-GCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGGgtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv05s0020g04510.t01 (Vitis vinifera), 5'ss of exon 4
TGCA-CTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatagattgagatcttcttc---------ttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag----------------
 ||| |||| ||| | |||||||||||||| ||||| ||||| || ||||| ||||||||||| ||||| || || |||||||| |||||||| ||||||||| || |   | ||||  ||    ||          ||  | |||    |    |||| ||  |||  | |   |                         
-GCAACTGAGGAGTTATGCAAGCACTACACTAAGGACTTTGGAATTGAGTGTCGCATTGGACGGTTCCATAATATATATGGACCTTTTGGAACATGGAAAGgtcagcttgca-attgtaattccgtttggatgatggtttttccttctttccttttgggtgtttctgttaatacattttgtttctcctttttccattatag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S98_250V6.1 (Physcomitrella patens), 5'ss of exon 3
TGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcatag---attgagatcttcttc-ttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag-------------------------------------------------------------------------------
  ||| || ||| |||||||||| ||||| ||||| || || || |||||||| ||||| || |||||||||||||| |||||||  ||||| ||||| ||| ||   | ||   || || ||  ||    |  | ||  |  | |  |||     |  ||   |||   |                                                                                       
GCCACAGAGGAGTTGTGCAAGCATTACACAAAGGACTTCGGCATGGAGTGCCGAATTGGGCGTTTCCACAACATCTACGGACCCTACGGAACATGGAAGGgtaagcaaacagtccatcgaaattctccaaatcacctcactgacatt-gtgttcacatttgcatttgcggcttcttttcttttcttttctttcttgtgttttaagcttccctataggcctgttcattgaagccaagtatgagatttccttctgctcag

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S171_56V6.2 (Physcomitrella patens), 5'ss of exon 3
TGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtga--gttcataga--ttgagatcttcttc-ttgcttctttagc-ctgagtgggagtaactgagattgtttcaaaaccag-------------------
  ||| || |||||||| | |||||| || ||||| || || || ||||| |||||||| || |||||||||||||| || |||| |||||||||||| ||| |   ||| ||    |     || | |||  |   |||| |   |||| |   | |      | |||      |  |||                   
GCCACGGAGGAGCTGTGTAGGCACTATACAAAGGACTTCGGCATGGAGTGTCGCATTGGTCGTTTCCACAACATCTACGGTCCCTATGGAACCTGGAAGGgtaataattcgtaaggctcctcgtcattttcactatctcttaaaaactgatttcaaatctacatgtttgcaatgcagtcagaagaatcctcattttgagc

upper sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S237_14V6.1 (Physcomitrella patens), 5'ss of exon 3
TGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttca---tagattgagatcttctt-cttgcttctttagcctgagtgggagtaactgagattgtttcaaaaccag-------------------------------------------------------------------------------
  ||| || ||| ||||||| || ||||| ||||| ||||| || |||||||||||||| || || |||||||| ||||| || |  ||||||||||| ||| ||| ||    |||||      |  ||  |  ||| ||||  ||   |     || || | || |    |  |  |                                                                                
GCCACCGAGGAGTTGTGCAAACATTACACGAAGGACTTTGGCATGGAGTGCCGCATTGGTCGCTTTCACAACATTTATGGCCCATACGGAACCTGGAAGGgtaagtacaggagagattcgcccatcattattcacttttttaatctctttaaacttatctcaaatcgaagtatcattaatgtagtcagatgtacttgtgttttgccttgattctttctcgagggttctgagtaaccattgttgagcttgcctgtacag

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: 33 (upstream exon), 30 (downstream exon)
Score: 4

TGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGAACCTGGAAAGgtgagttcat ... tcaaaaccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC




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