Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtgaacgttttgttagtggatttttgatgtttttggtccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ20694 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ20694 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA06G12010.1 (Glycine max), 3'ss of exon 9
----------------------------------------------gtaagtgtgaacgttttgttagtgg--atttttgatgtttttggtccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG
| | | | || | | | || | | | | || | |||| ||||| || || |||| || || || || ||| | ||||||||||| || |||||||| ||||||||||| |||||||| | |||| |||||| |
attatgatatctatagatatggatataacattgttaatcaatatttcttattttttgttttgaatcaataatcatgtgtattttcctttacctggtgcagCTTGTCGTTGATACTTTGCCATTTGGGGGAGTTGGGGAGAGTGGAATGGGTGCATACCATGGGAAGTTCTCTTTTGATGCTTTTACACACAAAAAGGCAG
upper sequence: EFJ20694 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA04G42740.1 (Glycine max), 3'ss of exon 9
-----------------------------------------gtaagtgtgaacgttttgttagtggatttttgatgtttttggtccttc-------gcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG
| | | ||| | | | |||||| |||| | | ||||| |||| |||| || || |||| || || || || ||| | ||||||||||| || |||||||| ||||||||||| |||||||| | |||| ||| || |
ataggcattttgcattgttatttaaaaatccttattttctgtttcatatcaacttaaaatctgaacatttttcatgtgtattctccttttcctggtgcagCTTGTGGTTGATACCTTGCCATTTGGGGGAGTTGGGGAGAGTGGAATGGGTGCATACCATGGGAAGTTCTCTTTTGATGCTTTTACACACAAAAAAGCAG
upper sequence: EFJ20694 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------------------gtaagtgtg-aacgttttgttagtggatttttgatgtttttggtccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG
||| | ||||| | | | | || | || | |||||||| |||| | ||||| || || || || | ||||||||||| | |||||||| |||||||||| || ||||||||||| |||||| | |
taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAGMapped 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|169104982|gb|FE506591.1|FE506591EST: TCAGCGAAACATCAGCGGGAGGCATGGTTGTCAATGACACAGTTTTACAT TTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGG
genomic: TCAGCGAAACATCAGCGGGAGGCATGGTTGTCAATGACACAGTTTTACATgtaagtgtga ... tccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGG
EST:
gi|169049211|gb|FE459487.1|FE459487EST: TCAGCGAAACATCAGCGGGAGGCATGGTTGTCAATGACACTGTTTTACAT TTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGG
genomic: TCAGCGAAACATCAGCGGGAGGCATGGTTGTCAATGACACAGTTTTACATgtaagtgtga ... tccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGG
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:
9TCTGGCCCTCTATCTCTTCACTCGCGACAAAGCTCTGGAGAAGAAGGTGGTCAGCGAAACATCAGCGGGAGGCATGGTTGTCAATGACACAGTTTTACATgtaagtgtga ... tccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaagtgtgaacgttttgttagtggatttttgatgtttttggtccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG
ttttgat putative branch site (score: 9)
tccttcgc putative PPT
atttttgatgttttt TA-rich tract