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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGGTTACATTGCTGGAATTTTTTGCGCTATCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatccttgttttcttcttgttcttgcgcttatttcgttatcttttgctccag

Basic information

species Selaginella moellendorffii
transcript EFJ34707
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34707 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os09g28160.1 (Oryza sativa), 5'ss of exon 3
TGGCGGTTACATTGCTGGAATTTTTTGCGCTATCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtat---ccttgtt------ttcttcttgttcttgcgcttatttcgttatcttttgctccag---------------------------------------------
  | || |||||||||||| | || |||||   |||||||||||||||||||||| | |||||||| ||||||||  |||||| ||| ||| ||||  | ||| || |   || |||         |  |  |    |   |||   | | |   ||||||    |                                             
GAGTGGCTACATTGCTGGAGTCTTCTGCGCCGCCGTCTCGCACCCTGCTGACAACTTGGTCTCGTTTCTCAACAACTCCAAGGGCGCCACCGTTGGAGATgtaagtctgcaccctgtagaacggcacagccgggagctatacttgacttgatgcgttttgccaatgtgtgattgttttgtgttcgtttgctgaattcttatttcttttcag

upper sequence: EFJ34707 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os04g37600.1 (Oryza sativa), 5'ss of exon 4
TGGCGGTTACATTGCTGGAATTTTTTGCGCTATCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatccttgttttcttcttgttctt------gcgcttatt----tcgttatcttttgctccag------
 || ||||||||||| ||  | || || || || || || |||||||| ||||| ||||| || |||||||||||| |||||| ||||||  ||||| | ||| || |  |  |   | |    |  |       | | || ||    |  |||| | ||| | ||       
AGGTGGTTACATTGCAGGGGTGTTCTGTGCAATAGTTTCACACCCTGCGGACAATCTTGTGTCTTTCCTCAACAATGCCAAGGGCGCAACAGTTGGCGATgtaagttttgtaatcaccataccatcttctgtaacgtgtttgttggatttattatttcttgttgcatttacag

upper sequence: EFJ34707 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv17s0000g00400.t01 (Vitis vinifera), 5'ss of exon 4
TGGCGGTTACATTGCTGGAATTTTTTGCGCTATCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatccttgttttct-tcttgttcttgcgcttatttcgttatcttttgctccag--------------------------------------
||| || ||  | ||||| || || || |||||||| || ||||||||||||||||| ||||| || || |||||| ||||||  || ||  | ||  | ||  ||   ||   ||  | ||   ||  ||    ||| |    | || |  |                                           
TGGTGGATATGTGGCTGGTATATTATGTGCTATCGTGTCACACCCTGCTGACAACCTGGTCTCTTTTCTGAACAATGCCAAGGGGGCGACTGTGGGTGATgtgagtgaactaacttcttatcgatttgatggatctatatatacacctctccccttgatctcacccactttgttttgatgtatttccatggtgcag

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|169045763|gb|FE451190.1|FE451190
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAA                         GCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
EST: gi|169115022|gb|FE516387.1|FE516387
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAA                         GCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
EST: gi|169035004|gb|FE444852.1|FE444852
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAA                         GCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
EST: gi|169040864|gb|FE447915.1|FE447915
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAA                         GCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
EST: gi|169050328|gb|FE457550.1|FE457550
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAA                         GCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
EST: gi|169099376|gb|FE500992.1|FE500992
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAA                         GCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTG

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: 24

TGGCGGTTACATTGCTGGAATTTTTTGCGCTATCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCAACCATTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCCGGTGGCTCTCTTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACACTCACTGGAGCACAGTGGGGAATCTACG




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