RetrogeneDB ID: retro_cpor_1202

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_56:8088104..8088697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ2
• Ensembl ID: ENSCPOG00000011458
• Aliases: None
• Description: None

Sequence

>retro_cpor_1202
GTTTTTCTCAGGGGACAGTTGACCTACACACTGGATGTCTTTCTGTGTCTAAATTACTGTCGAATAGCTCTGGGAGCAGC
ATTGTTACTACTCTCATCACCTACCCACCTGTAAAGAGAATCACCTACTGGCCTCAGCTAGCCTTGGGGTTGATTTTTAG
TTGGGAGCACACTGCTTGACTGTTTAGCTATAAAGCACTCCTATTACCTATCCATGTGCCTGTCTCTCTGCTTTTCTGGA
GCTATGAGGCACTGATCTCTGTTATTATTTATTCCCATCAGGCCAAAAGAGATGATTTTCTGATCAACCTCAAGTCCATG
GCACTGGAGTTCACAGAAAACACCTAGCGGTGGGCTCAGTGGTTTCTGTATGGCCATGCAGGCAGCGCTGAACCAAGTTG
GCATCAGCTGTGTACAGATCTTTCCATACTGCACTGCTTTCATTTTTGGGGCCCATGTGGCTCACCAGATACACACTCTG
GATATCCACAACCTTGGAGAATGTTGGGTTACATACCTCCCAACTAAACAATAAGAATAACTCTCTTGTTCAGAATTATC
CTCAAAAATTTGCAGAAAGAAAAGATAGATGAA

Alignment

ORF - retro_cpor_1202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.9 %
• Parental protein coverage: 55.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VFLGGQLTLALCVLLCLNYYSIALGAASLVL-VITYPLMKRVTYWPQLALGLTFNW-GALLGWSAVRGSC
          VFL.GQLT..L.V.LCLNY..IALGAA.L.L..ITYP..KR.TYWPQLALGL.F.W...LL...A...S.
Retrocopy VFLRGQLTYTLDVFLCLNYCRIALGAALLLL<LITYPPVKRITYWPQLALGLIFSW>STLLDCLAIKHSY

Parental  DLSVCLPLYFAGVM-WTLVYDTIYAHQDKRDDALIGLRSTALLFREDTKYW-LGGFSVAMLGALSLVGAS
          .LS.CL.L.F.G.M...L....IY.HQ.KRDD.LI.L.S.AL.F.E.T..W.L.GF..AM..AL..VG.S
Retrocopy YLSMCLSLCFSGAM<EALISVIIYSHQAKRDDFLINLKSMALEFTENT*RW>LSGFCMAMQAALNQVGIS

Parental  CAQTPPYYAALLAVAAHLAHQIRTLDIHSPADCWDKF-SSNRTVGIILFLGIILGNLWKEKTDK
          C.Q..PY..A.....AH.AHQI.TLDIH....CW......N.T..I.L...IIL.NL.KEK.D.
Retrocopy CVQIFPYCTAFI-FGAHVAHQIHTLDIHNLGECWVTY<PPN*TIRITLLFRIILKNLQKEKIDE

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	13.23 RPM
SRP017611_kidney	0.00 RPM	29.84 RPM
SRP017611_liver	0.00 RPM	10.01 RPM
SRP040447_lung	0.00 RPM	16.32 RPM
SRP040447_skeletal_muscle	0.00 RPM	16.53 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1202 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1202 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 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005006	1 retrocopy	retro_amel_1898,
Bos taurus	ENSBTAG00000005744	1 retrocopy	retro_btau_1835,
Cavia porcellus	ENSCPOG00000011458	1 retrocopy	retro_cpor_1202 ,
Equus caballus	ENSECAG00000012542	1 retrocopy	retro_ecab_432,
Myotis lucifugus	ENSMLUG00000015267	1 retrocopy	retro_mluc_1776,
Mus musculus	ENSMUSG00000029319	1 retrocopy	retro_mmus_2883,
Tarsius syrichta	ENSTSYG00000013801	30 retrocopies	retro_tsyr_1015, retro_tsyr_1155, retro_tsyr_1173, retro_tsyr_1180, retro_tsyr_1207, retro_tsyr_1235, retro_tsyr_1327, retro_tsyr_1335, retro_tsyr_1385, retro_tsyr_1451, retro_tsyr_1491, retro_tsyr_1646, retro_tsyr_1709, retro_tsyr_1742, retro_tsyr_2015, retro_tsyr_2062, retro_tsyr_2087, retro_tsyr_2136, retro_tsyr_2146, retro_tsyr_466, retro_tsyr_513, retro_tsyr_533, retro_tsyr_54, retro_tsyr_548, retro_tsyr_607, retro_tsyr_619, retro_tsyr_654, retro_tsyr_776, retro_tsyr_839, retro_tsyr_995,
Tursiops truncatus	ENSTTRG00000005647	1 retrocopy	retro_ttru_1726,