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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCCCGCTGGAAGCGATCTCCAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccgacacatcctctctgtagatgccgctctaatgtccgcgacgatcgtgtag

Basic information

species Selaginella moellendorffii
transcript EFJ36013
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36013 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os05g11560.2 (Oryza sativa), 5'ss of exon 2
AATTCCCGCTGGAAGCGATCTCCAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccgacacatcctc--tctgtagatgccgctctaatgtccgcgacgatcgtgtag----------------------------------------
    || || ||   |||  | |||||| |     ||||    |||||||||| |   ||||||||||||||||||| |||||||||||||   ||||| || ||    ||  | ||  |   |  |   ||    | ||   |   | |     ||  |                                         
GGCGCCGGCCGGGTCCGACGTGCAGTCGCTGGCGATGGAGTTCATCATCACCTTCTACCTCATGTTCGTCGTCTCCGGCGTCGCCACCGACAACCGAGCTgtgagt-ttgatccttctccaaaccattcttgttcttgtacgttttccaaactgtgttcaatgttacctcttccgaactgttccctcgtactagtagtttt

upper sequence: EFJ36013 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os01g10600.1 (Oryza sativa), 5'ss of exon 5
AATTCCCGCTGGAAGCGATCTC-CAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccgacacatcctctctgtagatgccgctcta---atgtccgcgacgatcgtgtag----------------------
     |||  ||   ||||  | ||| ||      |||||     ||||| ||| | | ||||||||||||||||||| ||||||||| |||    |||| |||   |     ||| |    ||    |     || ||   || | |  || |||||   |                       
-GACGCCGGCGGGGTCGATGGCGCAGGCGGCGGCGCTGGAGTTCGTCATCTCCTTCTTCCTCATGTTCGTCGTCTCCGGCGTCGCCACGGACAACAGAGCAgtataagatcgaacaccaaaactaacaaattaactatatatatatgcatgatgatcgatgataattttgtggtgtacaacacag

upper sequence: EFJ36013 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
AATTCCCGCTGGAAGCGATCTCCAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccgacacatcctctctgtagatgccgctctaatgtccgcgacgatcgtgtag----------------------------------------------------------------------------------------------------------------------------
  | ||||| ||   |||  | |||||| ||   || ||    |||||||||| |   |||||||||||| |||||| |||||||||||||   ||||| ||||||  |    ||   | |   |  ||     |  | ||  | |  || |  |  |                                                                                                                             
GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag

upper sequence: EFJ36013 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G126582_T01 (Zea mays), 5'ss of exon 2
AATTCCCGCTGGAAGCGATCTCCAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccgacacatcctctctgtagatgccgctctaatgtccgcgacgatcgtgtag---------------------------------------------
  | ||||| ||    ||    |||||| ||    | ||    |||||| ||| ||  ||||||||||||||||||| ||||||||| |||    |||| ||||||||| |  |||  |     ||  | |  |   ||  ||  |   ||| ||  |                                              
GGTGCCCGCCGGCTCGGACGCGCAGTCGCTCGTCGTCGAGTTCATCATCTCCTTCAACCTCATGTTCGTCGTCTCCGGCGTCGCCACGGACAACAGAGCCgtaagcgccaaaccatgattatatta--tactacatgaaattcttc--tgattgttcaacctcgacgacgatctctccgtccgtcacgggtcctgcttagctgc

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|169102850|gb|FE508634.1|FE508634
EST:     CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCG                         ATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
genomic: CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
EST: gi|169040417|gb|FE448430.1|FE448430
EST:     CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCG                         ATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
genomic: CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
EST: gi|169102851|gb|FE508635.1|FE508635
EST:     CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCG                         ATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
genomic: CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
EST: gi|169054254|gb|FE463195.1|FE463195
EST:     CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACACTCGAGCG                         ATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
genomic: CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
EST: gi|169039915|gb|FE447601.1|FE447601
EST:     CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCG                         ATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
genomic: CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
EST: gi|169054253|gb|FE463194.1|FE463194
EST:     CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACACTCGAGCG                         ATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC
genomic: CCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCC

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), 34 (downstream exon)
Score: 18

AATTCCCGCTGGAAGCGATCTCCAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccg ... gatcgtgtagATTGGAGAATTGGCAGGCCTCGCAATCGGTGCTACAGTGGGCTTGAATGCCATCTTCGCCGG




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