RetrogeneDB ID: retro_cpor_1435

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_83:2391395..2391921(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SUMF1
• Ensembl ID: ENSCPOG00000014854
• Aliases: None
• Description: None

Sequence

>retro_cpor_1435
AAGTGGGATGAGACAGCAACCACAAGGACAGTCGCTATTGATACCTTTTACATGGATGCCTGTGAAGTCCATAATGCTGA
ATTGTAGCAGTTTGTGAACTCAACTGGCTGTTTGACAGAGTCTGAGAACTTTCATGACTCCCTGGTCTTTGAAGGCATAT
TGAGTGAGCAAGTGAAGCCTGATATCTACAGGCAGTCTCAGCTGCTCCCTGTAGTTACCTGTTACAGGCACCAACTGGAG
ACTCACAGAGGGGCCTGACTTCACTTTGAGCATAGCCCAGGGCATCCAGGGCTCAGCGCCTCCCAGAATCACTCAGCTGC
CTACTGCATGTGGGCAGGGAGGTGGCTGCCTGTGAAAGCTGAGTGGGAGAACAGTTGTGAGGAGGCCTACAGGACAGGCT
TTTCCCCTCTGGCAACAAACTGCTACCAAAAGACTATCATACGCCAACCTCTGGCATGGTGAGCTCCCTGTGACCAACAC
GGGGGGAGACATGTTCTCAGGGACAACACCTGTTAATGCCTTTCCT

Alignment

ORF - retro_cpor_1435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.74 %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KQDGEAPARRVTIDAFYMDAYEVSNAEFEKF-NSTGYLTEAEKFGDSFVFEGMLSEKVKTDIQ-QAVAAA
          K.D..A..R.V.ID.FYMDA.EV.NAE...F.NSTG.LTE.E.F.DS.VFEG.LSE.VK.DI..QAV.AA
Retrocopy KWDETATTRTVAIDTFYMDACEVHNAEL*QFVNSTGCLTESENFHDSLVFEGILSEQVKPDIY<QAVSAA

Parental  PWW-LPVKGANWRHPEGPDSTI-QHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCR-GGLQNRLF
          P...LPV.G.NWR..EGPD.T...H.P.HP.L..S.N...AYC.WAG..LP..AEWE.SC..GGLQ.RLF
Retrocopy PCS<LPVTGTNWRLTEGPDFTL<EHSPGHPGLSASQNHSAAYCMWAGRWLPVKAEWENSCE<GGLQDRLF

Parental  PWGNKLKPKGQH-YANLWQGEFPVTNTGEDGFQGTAPVDAFP
          P.GNKL.PK..H.YANLW.GE.PVTNTG.D.F.GT.PV.AFP
Retrocopy PSGNKLLPKDYH<YANLWHGELPVTNTGGDMFSGTTPVNAFP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	6.38 RPM
SRP017611_kidney	0.00 RPM	39.89 RPM
SRP017611_liver	0.00 RPM	26.29 RPM
SRP040447_lung	0.00 RPM	22.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1435 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1435 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039855	1 retrocopy	retro_btau_1116,
Cavia porcellus	ENSCPOG00000014854	1 retrocopy	retro_cpor_1435 ,