RetrogeneDB ID: retro_cpor_774

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:5520771..5521418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND5
• Ensembl ID: ENSCPOG00000005076
• Aliases: None
• Description: None

Sequence

>retro_cpor_774
CAAACAAGGATGGCTCAGGAGACTAGTCAGACTCCAGGGCCCATGCTGTCTAGTACAGGATGTGGCTTTTATGGGAACTC
TAGGACAAATGGAATGTGTACTGTTTGCTACCAAGAACATCTTCAGAGGCAGCAGAATAGTGGCAGAGTGAGCCCAATGG
GGACAGCCAGTGGTTCTCACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGACCCTAGGTTAAGCAATTGTGAA
GGTGCTGCTGGCAGCACATCTGAAAAATCAAGAAATATGCCTGTGGCTGCCTTGCCTGTAACTCAGCAAATGACAGAAAT
GAGCATTTCAAGAGAGGACAAAATAACTACTCCAAACATAGGTGTCAGAGCCAGTTGTTACTCAGCCCATTCTATTAGTT
TCTCAGCCCAGTACTTCTAAAAGTGAAGAAAAAGCTCCTGAATTGCCCAAACCAAAGGAGAGCAGATGTTTCACGTGTAG
AAAGAAAGTTGATCTTACAGGATTTGACTGCTGATGTGGGAATTTGTTTCATGGACTTCACCATTGCTCTGACAAGCACA
ACTGCCCATATGATTACAAAGCAGAAGCTGCAGCAAAAAGCAGAAAAGAAAATACAGTTGTTGTGGCTGAAAAAAATCCA
GAGAATA

Alignment

ORF - retro_cpor_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTRMAQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQQNSGRMSPMGTASGSNSPTSDSASVQ
          QTRMAQET.QTPGPML.STGCGFYGN.RTNGMC.VCY.EHLQRQQNSGR.SPMGTASGS.SPTSDSASVQ
Retrocopy QTRMAQETSQTPGPMLSSTGCGFYGNSRTNGMCTVCYQEHLQRQQNSGRVSPMGTASGSHSPTSDSASVQ

Parental  RADTSLNNCEGAAGSTSEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVS-QPST
          RAD..L.NCEGAAGSTSEKSRN.PVAALPVTQQMTEMSISREDKITTP...V........S.S.S..P..
Retrocopy RADPRLSNCEGAAGSTSEKSRNMPVAALPVTQQMTEMSISREDKITTPNIGVRASCYSAHSISFS<SPVL

Parental  SQSEEKAPELP-KPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKAEAAAKIRKENPVV
          .....K....P.KPK..RCF.CRKKV.LTGFDC.CGNLF.GLH..SDKHNCPYDYKAEAAAK.RKEN.VV
Retrocopy LKVKKKLLNCP<KPKESRCFTCRKKVDLTGFDC*CGNLFHGLHHCSDKHNCPYDYKAEAAAKSRKENTVV

Parental  VAE-KIQRI
          VAE.KIQRI
Retrocopy VAE>KIQRI

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	68.85 RPM
SRP017611_kidney	0.00 RPM	28.89 RPM
SRP017611_liver	0.00 RPM	36.82 RPM
SRP040447_lung	0.00 RPM	39.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	54.82 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_774 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_774 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774 ,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23,