RetrogeneDB ID: retro_cpor_951

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_36:8150720..8151587(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000019632
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ALDOA
• Ensembl ID: ENSCPOG00000007434
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:H0VA39]

Sequence

>retro_cpor_951
TACCCATATCCAGCACTGACTCCAGAGCTGAAGAAAGAGGTATTTGACATTGATCACTACACTGTGGCCCTGGGCGAGGG
CATCCTCACTGCAGATGAGTCCCCTGGAAGCGTTGCCAAGCAGCTGCAGTCTATTGACACTGAGAACCCCAGAGAAACTG
GCGCTGCTACACCAGCTGCTGTTGATGCTGATAACTCTGTGAATCCCTGCACTGAGGTGTCATCTTTTCCATGGGATGCT
GTACCAGAAAGCAACTGATGCACATCCATTCCCCCAAGTCATCAATTCTAAGAGTGGTGTCATGGGCATCAAGGTAGACA
AGGGTATGATGCCCCTGGTAGGAACAAACGGTGAGACCATCACCCAGAGACTGGATGGGCTGTCTGAGCACTGCCACCAG
TACAAGAAGGATGGAGCTGACTTTGCCAAGTGGTTCTGGATGCTGAAGATTGCAGAACACATCCCTGCAGCCTTGCCATC
ATGGAGAATGCCAACATCCTGGCTCCTTTGCAGCAGAATGGCGTTGTGCCCATTGGGGAGTCTGAGAATCTTCTTGATGG
GGACCACCACTTGGAGAATTGTCATCTTGTAACCAAGAAGGTGCTTGCTGCTTGCTGTCTACAAGGCTCTGAGTGACCAT
CACATCTATCCGGAAGGCACCTTGCTGAGTGCCAACCTGGCCAAGTCTGCACCCAGGAGTATTCCCATGAGGAGATTACC
ATGGCAACTCTCACAGCACTGTGCCCCACAGTGTCACACCCTGCTATCACTGGGATTATCTTCCTGTTTGGAGGACAGAG
AAAGGAGGATGCATCAGCCATGGACCGTGACCTTCTCCTATGTCAGGCCCTGCAGGCTTCTGCACTA

Alignment

ORF - retro_cpor_951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.74 %
• Parental protein coverage: 81.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  HQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEE-NRRFY-RQLLLT-ADDR
          ..YPALTPE.KKE..DI.H..VA.G.GIL.ADES.GS.AK.LQSI.TEN..E.N.R.Y..QLLL..AD..
Retrocopy YPYPALTPELKKEVFDIDHYTVALGEGILTADESPGSVAKQLQSIDTENPRE<NWRCY<HQLLLM<ADNS

Parental  VNPCIG-GVI-LFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQ
          VNPC...GVI.LFH..LYQKA.D..PFPQVI.SK.GV.GIKVDKG..PL.GTNGET.TQ.LDGLSE.C.Q
Retrocopy VNPCTE<GVI<LFHGMLYQKATDAHPFPQVINSKSGVMGIKVDKGMMPLVGTNGETITQRLDGLSEHCHQ

Parental  YKKDGADFAKWRCVLKIGEHTPSAL-AIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVT
          YKKDGADFAKW...LKI.EH.P.AL.AIMEN....A......QQNG.VPI.E.E.L.DGDH.L..C..VT
Retrocopy YKKDGADFAKWFWMLKIAEHIPAAL<AIMEN----ANILAPLQQNGVVPIGESENLLDGDHHLENCHLVT

Parental  EKVLAAVYKALSDHHVYLEGTLLKPNMVTAGHACTHKYSHEEIAMATVTALRRTVP-PAVTGITFLSGGQ
          .KVLAA.....S.....L.G..L.......G..CT..YSHEEI.MAT.TAL..TV..PA.TGI.FL.GGQ
Retrocopy KKVLAACCLQGSE*PSHLSGRHLAE--CQPGQVCTQEYSHEEITMATLTALCPTVSHPAITGIIFLFGGQ

Parental  SEEEASINLNAINKCPLLKPWAL
          ..E.AS........C..L...AL
Retrocopy RKEDASAMDRDLLLCQALQASAL

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	677.14 RPM
SRP017611_kidney	0.00 RPM	578.29 RPM
SRP017611_liver	0.00 RPM	47.31 RPM
SRP040447_lung	0.00 RPM	618.87 RPM
SRP040447_skeletal_muscle	0.00 RPM	11296.20 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_951 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_951 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 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951 ,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,