RetrogeneDB ID: retro_cpor_144

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:83137605..83138422(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSCPOG00000002424
• Aliases: None
• Description: None

Sequence

>retro_cpor_144
CTCTGGTCTGTGATGAAGGTGGAAAAGGCCCCCCAGGAAGCCTATGCCAACATTGGTGGGTTGGACAACCAAATGCAAGA
AATTAAGGAATCTGTGGAGCTTCCTCTCACCCATCCTGAATACTATGAAGAAATGGGTATAAAGCCCTCTAAGGGCGTCA
TTCTCTATCGTCCGCCTGGCACAGGTAAAACCTTGTTAGCCAAAGCAGTAGCAAACCAAACTTCGGCCACTTTCTTGAGA
GTGGTTGGCTCTGAACTTATTCAAAAATACCTGGGCGATGGGCCCAAACTTGTATGGGAATTATTTCGAGTTGCTGAAGA
ACATGCACCATCCATCGTGTTCATTGATGAAATCGATGCCATTGGGACCAAAAGATACGATTCAAACTCTGGAGGTGAGA
GAGAAATTCAGTGAACAATGTTGGAACTGCTGAACCAGTTGGATGGATTTGTTTCATGGGGAGACATGAAAGTTATCATG
GCCACAAACCAAATAGAGACTTTGGATCCAGCACTGATCAGACGAGGCCGCATGGACAGGAAGATCGAGTTCCGCTTGCT
CCATGGATGAAAAGACCAAGAAGGCATCTTTCAGATCCACACAAGCAGGATGACACTGGCCGATGATGTAACCCTGGACG
ACCTGATCATGGTGAAGGACAATCTCTCTGGGTGCTGACATCAAGGCAATCTGTACAGACGCTGGTCTGATGGCTTTGAG
AGAACGTACAATGAAAGTAACAAATGAAGACTTCAAGAAATCTAAAGAAAATGTTCTTTATAAGAAACAGGAAGGGACCC
CTGAGGGGCTGTATCTC

Alignment

ORF - retro_cpor_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• Parental protein coverage: 61.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAV
          L..VMKVEKAPQE.YA.IGGLDNQ.QEIKESVELPLTHPEYYEEMGIKP.KGVILY.PPGTGKTLLAKAV
Retrocopy LWSVMKVEKAPQEAYANIGGLDNQMQEIKESVELPLTHPEYYEEMGIKPSKGVILYRPPGTGKTLLAKAV

Parental  ANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTM
          ANQTSATFLRVVGSELIQKYLGDGPKLV.ELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQ.TM
Retrocopy ANQTSATFLRVVGSELIQKYLGDGPKLVWELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQ*TM

Parental  LELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE-KTKKRIFQIHTSRMTLADDV
          LELLNQLDGF.S.GD.KVIMATN.IETLDPALIR.GR.DRKIEF.L....K....IFQIHTSRMTLADDV
Retrocopy LELLNQLDGFVSWGDMKVIMATNQIETLDPALIRRGRMDRKIEFRLLHG*KDQEGIFQIHTSRMTLADDV

Parental  TLDDLIMAKDDLS-GADIKAICTEAGLMALRERRMKVTNEDFKKSKENVLYKKQEGTPEGLYL
          TLDDLIM.KD.LS.GADIKAICT.AGLMALRER.MKVTNEDFKKSKENVLYKKQEGTPEGLYL
Retrocopy TLDDLIMVKDNLS>GADIKAICTDAGLMALRERTMKVTNEDFKKSKENVLYKKQEGTPEGLYL

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	0.06 RPM	56.54 RPM
SRP017611_kidney	0.00 RPM	84.69 RPM
SRP017611_liver	0.04 RPM	84.88 RPM
SRP040447_lung	0.00 RPM	68.32 RPM
SRP040447_skeletal_muscle	0.01 RPM	77.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_144 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_144 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 11 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Cavia porcellus	ENSCPOG00000002424	1 retrocopy	retro_cpor_144 ,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Ictidomys tridecemlineatus	ENSSTOG00000001655	1 retrocopy	retro_itri_780,