Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtaggcaacttctttgttggggcggtcgtttacgtagtaacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ10962 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------------gtgcgtaggcaacttctttgttggggcggtcgtttacgtagtaacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA
| | || | || | | | | | | | | ||||| ||||||||||||||||| || || |||||||||||||| || || || || ||||| || || ||||| || || | | |
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagac--ctgactgaaaactggcttc-cagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
upper sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA10G01280.2 (Glycine max), 3'ss of exon 10
-----------------------gtgcgtaggca-acttctttgttggggcggtcgtttacgtagtaacgt-----ggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA
|| | || | || || | || | || || ||| | ||| | ||||||||| | | ||||| |||||||||||||| ||||| || ||||| |||||||| || ||||| || || | |
gtattataatgttatttttgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTACTGCAATACTCTCCAAATCTTCGATGCACAGCT
upper sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA02G01220.2 (Glycine max), 3'ss of exon 10
-------------------------gtgcgtaggcaacttctttgttggggcggtcgtttacgtag---taacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA
|| | | | || ||| | || | || | | | ||| | ||||||||| | | ||||| |||||||||||||| ||||| || ||||| |||||||| || ||||| || || | |
gtattgtaatgttatatttgcctgtccatttatgtgatat-ttcattgtgatattcatatatatgaaccttcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTACTGCAATACTCTCCAAATCTTCGATGCACAGCTMapped 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|169024805|gb|FE435484.1|FE435484EST: ACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG GTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTA
genomic: ACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAGgtgcgtaggc ... aacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTA
EST:
gi|169105181|gb|FE504853.1|FE504853EST: ACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG GTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTA
genomic: ACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAGgtgcgtaggc ... aacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTA
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),
34 (downstream exon)
Score:
29GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAGgtgcgtaggc ... aacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcgtaggcaacttctttgttggggcggtcgtttacgtagtaacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA
tagtaac putative branch site (score: 29)