RetrogeneDB ID: retro_cpor_1226

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_59:4400093..4400654(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMZ2
• Ensembl ID: ENSCPOG00000013061
• Aliases: None
• Description: None

Sequence

>retro_cpor_1226
AAATTAATGAAGCCTTCCTGCCAGCCAGTGATAGCTGGGTCCATTATCTTGCATCTACAGTCAGATTGGATTATTTCCCA
TCCTGAGGTTCTCCAAGACTTTGAACAGTTTTTCAGGGATCCCTACGAAAAGACACCCTCTGCAGATGCATGCAGTATTT
ACATATAGTCTGTTGGAGTTCTCTGGAACATCAGAGTTATCAGTGAAGAATATGTTAAATGGCTCAAGTGCTACTGTGAA
GCATTTTTCTATGGGTTGACAGTAAAACTTCTAGAGCCAGTTTCTGTTTATGCAACCAGGTGTTCCTTTAGAGTCAATGA
TCATACACAAAATCTACAAATTCATGTAGGGCACATTTTGAATTTTTTAAAAAAACCTAAAGATACCATATGTGGTGTGG
ATATAAGAATGATTGATCTTTTGCCAAGAGACTTCTGGAATTTTGTCTTTGGACAGGTCTCTCTGACAGATGGTGTAGGA
GTATTCAAGTTCACCAGGTATGGCAGGGTTTTGTATGCCTCACTGTTTGAAGGTAAAGTGAAGAAGCTCCACCAAAAGAA
T

Alignment

ORF - retro_cpor_1226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.63 %
• Parental protein coverage: 53.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLMNEAFQPASELFGPITLHSQSDWITSHPEAPQDFEAFFSNPYRKTPSPEKHSIYIQSIGALGNTRVIS
          .LM....QP.....G.I.LH.QSDWI.SHPE..QDFE.FF..PY.KTPS....SIYI.S.G.L.N.RVIS
Retrocopy KLMKPSCQPV--IAGSIILHLQSDWIISHPEVLQDFEQFFRDPYEKTPSADACSIYI*SVGVLWNIRVIS

Parental  EEYIKWLKGYCEAFFYGLKVKLLEPVSVSATRCSFRVNDHTHNLQIHAGQILNFLKKKKPNDAFCVVGIT
          EEY.KWLK.YCEAFFYGL.VKLLEPVSV.ATRCSFRVNDHT.NLQIH.G.ILNFL..KKP.D..C.V.I.
Retrocopy EEYVKWLKCYCEAFFYGLTVKLLEPVSVYATRCSFRVNDHTQNLQIHVGHILNFL--KKPKDTICGVDIR

Parental  MIDLYPRDSWNFVFGQASLTDGVGIFSFARYGRDFYTSHYEGKVKKLQKKS
          MIDL.PRD.WNFVFGQ.SLTDGVG.F.F.RYGR..Y.S..EGKVKKL..K.
Retrocopy MIDLLPRDFWNFVFGQVSLTDGVGVFKFTRYGRVLYASLFEGKVKKLHQKN

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	95.07 RPM
SRP017611_kidney	0.00 RPM	68.67 RPM
SRP017611_liver	0.00 RPM	23.07 RPM
SRP040447_lung	0.00 RPM	34.45 RPM
SRP040447_skeletal_muscle	0.00 RPM	71.99 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1226 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1226 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009345	1 retrocopy	retro_btau_429,
Choloepus hoffmanni	ENSCHOG00000000493	1 retrocopy	retro_chof_2462,
Callithrix jacchus	ENSCJAG00000000254	1 retrocopy	retro_cjac_2798,
Cavia porcellus	ENSCPOG00000013061	1 retrocopy	retro_cpor_1226 ,
Equus caballus	ENSECAG00000011450	2 retrocopies	retro_ecab_440, retro_ecab_864,
Felis catus	ENSFCAG00000019195	1 retrocopy	retro_fcat_760,
Myotis lucifugus	ENSMLUG00000006771	2 retrocopies	retro_mluc_1540, retro_mluc_2056,
Mustela putorius furo	ENSMPUG00000014570	1 retrocopy	retro_mputfur_1224,
Pteropus vampyrus	ENSPVAG00000017239	2 retrocopies	retro_pvam_1453, retro_pvam_989,