RetrogeneDB ID: | retro_sscr_490 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 15:23679344..23680397(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KLF17 | ||
| Ensembl ID: | ENSSSCG00000024191 | ||
| Aliases: | None | ||
| Description: | Sus scrofa Kruppel-like factor 17 (KLF17), mRNA. [Source:RefSeq mRNA;Acc:NM_001164010] |
Retrocopy-Parental alignment summary:
>retro_sscr_490
ATGGAGCAGGGGGCCGAGGGCCTGAGCCAGTGGCCTGTGGCTCTGCACCAGCTTACAGAGGACACTGAGAAGTCACTGTC
CATCTTGGACATGTCTTCATCTCCAGGAAGCGGTGGAGTGCACACCTCTTGGAACCATGGCCCATCAGGCACTCAGCAGG
TTCCTCAGTGCACAGAGCTGGAGAGGATGTCCTTGGCCTCTGCTCAGGCACCCAGGCAGAATGCCTGTGAAATGGGGCAG
CAGTTCAGTATGTCACTTCCTGAGCATGGTGTGAGCTACTGCTCTCAAATGACTTTCACTGCTTCCCAGATGATTTACAG
TCAGGCAATGTCTCCTTCCCAGCCAGGAATGGGGGTTTTCAAGGGCTCCCAGGCAATGCCCTTAGGAGAGCCCAGTATTT
CAAGTGTGGGTGTGACCTTCAGTGGGAATCTAAGCATGCCCCCCAGTGGGCTGCCAGTCTCACCTCCCAGTGGAATCCCA
ATGATGTCCCACAATGGAATGCCAACAGTGCCTTATTCTGGCCTCCCAACAGTACTTTCCAACGGAGACTCTTTAACACC
TAAAATGTTTTTGGATCCAACCATGCCTTCCACTGAGGTTCAGGCAGTATTCCCCTCTTTGGCCCAGATGTTGCCCTCTA
GAGATCCTCAGGACTTTGGAATGCCCCCAGCTGGATCTCCATCACTGCTGGCTTTGGAATCCCAGGGCTCTCTTGCGAGC
CAGCCAGTCTCCCAGGAAGACTTTCCTAAGCACCGCTTATGTGCACCATGGACAGAGGCACAGAATTCCAGGGCCCAAGA
AAGGGCTTCCAGGAGGAGCTCTCCCATTTCAAGGCTTTACCATAGTAAGTACGAGAACTGCGGCAAAGCTTATATGAAGT
GCTCCCACCTCGTGAGTCACCAACGCAAACACACAGGTGACAGACCCTATAAATGCACGTGGGAAGCCTGTACCTGGTCC
TTTTTCCATTCCCTTGAACTTGGAAGGCATACTTGAATACACACCAGATATCGACCACATAAATGTGACCAGTGCAGCCA
ACAGTTCATGAGA
ORF - retro_sscr_490 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.32 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEQGAEGLSQWPVAPHQFTEDTEKSLSFLDMSSSPGSGGVHTSWNRGPSGIRRVPQCPELERMSLASAQA |
| MEQGAEGLSQWPVA.HQ.TEDTEKSLS.LDMSSSPGSGGVHTSWN.GPSG...VPQC.ELERMSLASAQA | |
| Retrocopy | MEQGAEGLSQWPVALHQLTEDTEKSLSILDMSSSPGSGGVHTSWNHGPSGTQQVPQCTELERMSLASAQA |
| Parental | PRQSACEMGQQFSMSPPEHGLSYCPQMTFTASQMVYSQGMSPSQPGMGAFKGAQAMPLGEPSISSVAVTF |
| PRQ.ACEMGQQFSMS.PEHG.SYC.QMTFTASQM.YSQ.MSPSQPGMG.FKG.QAMPLGEPSISSV.VTF | |
| Retrocopy | PRQNACEMGQQFSMSLPEHGVSYCSQMTFTASQMIYSQAMSPSQPGMGVFKGSQAMPLGEPSISSVGVTF |
| Parental | SGNLRMPPSGLPVSPPSGIPLMSHIGMPTMPYSGLPTVPFNGDALTPNMFLDPTMPPTEVQAVLPSLAQM |
| SGNL.MPPSGLPVSPPSGIP.MSH.GMPT.PYSGLPTV..NGD.LTP.MFLDPTMP.TEVQAV.PSLAQM | |
| Retrocopy | SGNLSMPPSGLPVSPPSGIPMMSHNGMPTVPYSGLPTVLSNGDSLTPKMFLDPTMPSTEVQAVFPSLAQM |
| Parental | LPSRDPQDFAMPPAGSPSLLPLESQGSFLSQPVSQEDFPKHHLCEPRREAQNSRAQERASGRSSPVSRPY |
| LPSRDPQDF.MPPAGSPSLL.LESQGS..SQPVSQEDFPKH.LC.P..EAQNSRAQERAS.RSSP.SR.Y | |
| Retrocopy | LPSRDPQDFGMPPAGSPSLLALESQGSLASQPVSQEDFPKHRLCAPWTEAQNSRAQERASRRSSPISRLY |
| Parental | HCEYENCGKAYTKRSHLVSHQRKHTGERPYKCTWEACTWSFFRSDELGRHTRIHTRYRPHKCDQCGRQFM |
| H..YENCGKAY.K.SHLVSHQRKHTG.RPYKCTWEACTWSFF.S.ELGRHT.IHTRYRPHKCDQC..QFM | |
| Retrocopy | HSKYENCGKAYMKCSHLVSHQRKHTGDRPYKCTWEACTWSFFHSLELGRHT*IHTRYRPHKCDQCSQQFM |
| Parental | R |
| R | |
| Retrocopy | R |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 0 .00 RPM |
| SRP014902_testis | 0 .00 RPM | 0 .14 RPM |
| SRP018288_heart | 0 .00 RPM | 0 .00 RPM |
| SRP018288_kidney | 0 .00 RPM | 0 .10 RPM |
| SRP018288_liver | 0 .00 RPM | 0 .00 RPM |
| SRP018288_lung | 0 .00 RPM | 0 .00 RPM |
| SRP018856_adipose | 0 .00 RPM | 0 .00 RPM |
| SRP035408_brain | 0 .00 RPM | 0 .00 RPM |
| SRP035408_liver | 0 .00 RPM | 0 .00 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_490 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_490 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_490 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Microcebus murinus | ENSMICG00000007300 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000024191 | 2 retrocopies |
retro_sscr_489, retro_sscr_490 ,
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