Sequence
atgc intronic sequence ATGC exonic sequenceTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttcttcgtgttttttctttgcttggcattacgcttgtgcttgcag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ21414 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 2
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagt--tcttcgtgttttttctttgcttggcattacgcttgtgcttgcag-------------------------------
| ||||||||||||||||||| ||| || || || ||||| | ||||| || || |||||| |||||||| ||||||||| ||||||| |||| | | | | || || |||| ||| | | | ||| ||
TGCCGTTTGAAGAGGATGACAAGGATCCGAGGATCTGGTTCCTCGATCATAATTACCACGAATCGATGTTTTCCATGTTCAAGAGGATCAACGgtatgcagtttgcaagtcttccatttgtttgacctgccctgtgtaactgattgtgttgtactgacgagctgttcttcgtgtag
upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttcttcgtgttttttctttgcttggcattacgcttgtgcttgcag---------------------------------
| || ||||| |||||||||| ||| ||||||| |||||| | ||||||||||| ||||| |||||||| | ||||||||| | || ||||||| || ||| | | | | |||| | || ||||
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgta--ttgctcgggaaatataat-gcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttct--------tcgtgttttttctttgcttggcattacg----cttgtgcttgcag---------------------
| || ||||| |||||||||| ||||||||||| |||||| | ||||||||||| || || | ||||| | ||||||||| | || ||||||| |||| | || || | || | || |||| ||||| |
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag
upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 2
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaa-gttcttcgtgtttttt----ctttgcttggcattac-----gcttgtgcttgcag--------------------
| || |||||||| ||||||| |||||||||||| |||||| | || ||||||||||| ||| | |||||| ||||||||| | || ||||||| || ||||| | | | |||| ||| || | ||| |
TGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgtttcagMapped 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|169103938|gb|FE504275.1|FE504275EST: GCGATGTTTGATATG-TCAAAGCGGATCAATG CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGA
genomic: GCGATGTTTGATATGTTC-AAGCGGATCAATGgtaagttctt ... gtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGA
EST:
gi|169103939|gb|FE504276.1|FE504276EST: GGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGA
genomic: GGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttctt ... gtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGA
EST:
gi|169057078|gb|FE464134.1|FE464134EST: GGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGA
genomic: GGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttctt ... gtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGA
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:
32 (upstream exon),
35 (downstream exon)
Score:
36TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttctt ... gtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA
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