RetrogeneDB ID: retro_cpor_616

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:2597481..2598142(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSCPOG00000011321
• Aliases: None
• Description: None

Sequence

>retro_cpor_616
TATGATGACATGACCACCTGCATGAAGTCAGTGACCAAGCAGGGCGCCAACCTGTCCAACTGGCTCTTGGTGGCCTACCA
GAAAGTGGTTGAGGGCTGCTGGTCAGCCTGGAGGGTCATCTCAAGCACCAAGTAGAAAACCAACACCTCCAACGAGAAGT
TGCTGCTGATTAGGGACCGGGGGGAGAAAGTGTAGTCCGGGTCCATCTGCACATGGTCCTGGGCTTGTTGGGTAAGTATT
TAACAGCCGGTGCAACTAATCCAGAGAGTAAAGTCTTCCATCTGAAAGTGAAGGGAGGCTACTTCCTATACCTGGCTGAA
GCTGCATGTGTTGATGATCGAGAACAAATAGATAATTCCCCAAGAGCTTCCAAGGGGCATTAGATATAGGCAAGAAAGAG
ATGCAGCCCCCACACCACATCCTCCCGGGACCGGCTCTTAACTTCTCTGTATTTTACTGTAAGATTCTTAATGACCCCGA
GCTTTCCTGCACACTGGCTAAGACAGCTTTTGATGAGGCCATAGCTGAGCTTGATACACTGAATGAAAACTCCTACCAAG
ACAGCAGCGCTCTCACCATGTAGCTGCTTAGAGACAACTTAACAGTGTGGACATCAGGCTGCACAGGAGAAGAATGTGAT
GTGGCAGGAGGGACCGAAAAC

Alignment

ORF - retro_cpor_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 96.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVES
          YDDM.TCMK.VT.QGA.LS....N.L.VAY..VV.G..SAWRVISS...KT.TS..KL.LI.D..EKV.S
Retrocopy YDDMTTCMKSVTKQGANLS----NWLLVAYQKVVEGCWSAWRVISSTK*KTNTSNEKLLLIRDRGEKV*S

Parental  ELRSICT-TVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGA-YQEAFDIS
          ...SICT..VL.LL.KYL.A.ATNPESKVF.LK.KG.YF.YLAE.AC.DDR.Q.IDNS..A..Q.A.DI.
Retrocopy G--SICT<MVLGLLGKYLTAGATNPESKVFHLKVKGGYFLYLAEAACVDDREQ-IDNSPRA<FQGALDIG

Parental  KKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDST-LIMQLLRDNL
          KKEMQP.H.I..G.ALNFSVFY..ILN.PEL.CTLAKTAFDEAIAELDTLNE.SY.DS..L.M.LLRDNL
Retrocopy KKEMQPPHHILPGPALNFSVFYCKILNDPELSCTLAKTAFDEAIAELDTLNENSYQDSSALTM*LLRDNL

Parental  TLWTSDSAGEECDAAEGAEN
          T.WTS...GEECD.A.G.EN
Retrocopy TVWTSGCTGEECDVAGGTEN

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	74.89 RPM
SRP017611_kidney	0.00 RPM	103.95 RPM
SRP017611_liver	0.00 RPM	22.20 RPM
SRP040447_lung	0.00 RPM	108.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.98 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_616 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_616 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008618	4 retrocopies	retro_amel_1214, retro_amel_1382, retro_amel_1837, retro_amel_917,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Cavia porcellus	ENSCPOG00000011321	4 retrocopies	retro_cpor_135, retro_cpor_1463, retro_cpor_616 , retro_cpor_668,
Cavia porcellus	ENSCPOG00000020285	5 retrocopies	retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,