RetrogeneDB ID: retro_cpor_393

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:6965160..6965837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004962
• Aliases: None
• Description: None

Sequence

>retro_cpor_393
TCTACCGCAGACCAAGGGGAGCCAGCTCTGCTCGGCGCCAACTTCTGCGACCTGGCTGTCAGCCCCACATCGCTGGCCTG
GAGGGGCGATGAGGATGAGGGAGCCCAGGCTTCCTCCGGGGCCATCAGCTCTCTGGGTTGTCAGGCGTTTGTAGTTGACA
TTGAGTCCAGGCTGAGGATGGAAGGTGTGGAACTGAAAAATAGTGGCAAGATGAAGATATTCTGATACCTTTACCAGAAG
ATGATAGTATTGAAGCAGATCTGCTCGATATACCTGGACCAGAGAACCATCCTGACTCACCAGAAGTAACAGAAATAAAG
TGAAAAAGAAATTAATGGCTCCAGACATCAGCCTGACACTGGAACCTAGCGATGGCTCTGTGTTGTCAGATGATTTGGAT
CAAAGTGGAGAGATCTACTTAGATGGCTTGGACACCCCATCAGAGAACAGTAATGAATGTGAGTGGGAAGGTGATCCTCC
AAAACCCAAACTACTGAAGTCATTAGGAAAGGCTCAGTGACTGAGCACACTCAGCAGAGGAGAAGGAGGACCGCGATGCT
GGCCGTGTTCAGATTGGCAAGCAGGACCACCGGGTTGACGTGAAGGCAATCGAGCCCTACAAGAAAGTCATCAGCCACAG
AGAATATTATGGGGATGGATTAAACGCCATTGTTGTG

Alignment

ORF - retro_cpor_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.45 %
• Parental protein coverage: 63.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STADRGERAPLGADFCDLAVSPTSPTWRGEEDEGAEAFSGALGSLGCQELAADIESRLRMEGVELKEE-W
          STAD.GE.A.LGA.FCDLAVSPTS..WRG.EDEGA.A.SGA..SLGCQ....DIESRLRMEGVELK...W
Retrocopy STADQGEPALLGANFCDLAVSPTSLAWRGDEDEGAQASSGAISSLGCQAFVVDIESRLRMEGVELKNS<W

Parental  QDEDFPIPLPEDDSIEADILGVPGPENQPDSPEV-NGNKVRKKLIAPDISLTLDPSDGSVLSDDLDESGE
          QDED..IPLPEDDSIEAD.L..PGPEN.PDSPEV.N.NKV.KKL.APDISLTL.PSDGSVLSDDLD.SGE
Retrocopy QDEDILIPLPEDDSIEADLLDIPGPENHPDSPEV<NRNKVKKKLMAPDISLTLEPSDGSVLSDDLDQSGE

Parental  VDLDGLDTPSENSNEFEWEDDLPKPK-TTEVIRKGSVTEYT-AAEEKEDGRRWRMFRIGEQDHRVDMKAI
          ..LDGLDTPSENSNE.EWE.D.PKPK.TTEVIRKGSVTE.T..AEEKED....R...IG.QDHRVD.KAI
Retrocopy IYLDGLDTPSENSNECEWEGDPPKPK<TTEVIRKGSVTEHT<SAEEKEDRDAGRV-QIGKQDHRVDVKAI

Parental  EPYKKVISHGGYYGDGLNAIVV
          EPYKKVISH..YYGDGLNAIVV
Retrocopy EPYKKVISHREYYGDGLNAIVV

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	8.28 RPM
SRP017611_kidney	0.00 RPM	9.00 RPM
SRP017611_liver	0.00 RPM	7.62 RPM
SRP040447_lung	0.03 RPM	28.47 RPM
SRP040447_skeletal_muscle	0.38 RPM	12.47 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_393 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_393 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014722	1 retrocopy	retro_cjac_2997,
Cavia porcellus	ENSCPOG00000004962	2 retrocopies	retro_cpor_393 , retro_cpor_935,
Mus musculus	ENSMUSG00000011958	1 retrocopy	retro_mmus_3251,