RetrogeneDB ID: retro_cpor_428

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:41383301..41383959(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025013
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL5
• Ensembl ID: ENSCPOG00000000698
• Aliases: None
• Description: None

Sequence

>retro_cpor_428
TGTTATTTGTCCTATTTTCTCATTTCTGTGTAGCAGGAGATATGCACAGCATCTGTGCACACACTACCATGATACGGTGT
GAAAGATGGCTTTACAACTCAGGCTGCAGCATATCCTATTGGCTTGCTGCAGGATTGCGGGCTTCTCAGAGGTTTGGCAC
TGACAAGATTTGTGAAGGCCAAGTGGAGGAGACAAGATGAATCCAATATCGAAAGCATTGATGGTCAGCCTGGTGCCTTT
ACCTGCTTTCTGGATGCTGGCTTTGCCACAACTACAACTGGCCGTAAAGTTTTTGGAGCCCTGGAGGGTGCTGTGGGTGG
AGGCTTATCTGTCCCTCACAGGACCGAATGGTTCTCTGGGTATGATTCAGAAAGCAAGGAGTTCAGTGCAGAAGCACATC
AAAAGCACATCATGGGTCAGAACATTGCAGATGATATGCGTTACCTACTGGGAAAAGACCAAGATGCTTAAGGAAACAGT
TCTCTCAGTACAGAAAGAACCATCTAACTGCAGACATACAGGAGGTATATAAGAAAGCTCATGCCGTGTGACACAACCAA
GTCCATGAAGAGAAGCTGAAGAAGTTAAAAAGATGGAGTGGAACTGTCCAAAAGTGTCCCTTGCCTAGAAGAAAGAGTGG
GTAGCTCAAAAGAAGGCA

Alignment

ORF - retro_cpor_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.82 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYN
          C...Y..I......C.A..H.LP.YGVK.G.T..AAAY..GLL....LL.................DE.N
Retrocopy CYLSYFLISV*QEICTASVHTLP*YGVKDGFTTQAAAYPIGLLQDCGLLRGLALTRFVKAKWR-RQDESN

Parental  VESIDGKPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
          .ESIDG.PGAFTC.LDAG.A.TTTG.KVFGAL.GAV.GGLS.PH.T..F.GYDSESKEF.AE.H.KHIMG
Retrocopy IESIDGQPGAFTCFLDAGFATTTTGRKVFGALEGAVGGGLSVPHRTEWFSGYDSESKEFSAEAHQKHIMG

Parental  QNVADYMRYLMEEDEDA-YKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYKKKPKREVKKKRWNR--
          QN.AD.MRYL...D.DA...KQFSQY.KN..T.D...E.YKKAH.A...N.V...K.K...K.KRW....
Retrocopy QNIADDMRYLLGKDQDA<LRKQFSQYRKNHLTAD-IQEVYKKAH-AV*HNQVHEEKLK---KLKRWSGTV

Parental  PKMSLAQKK-DRVAQKKA
          .K..L...K...VAQKKA
Retrocopy QKCPLPRRK<EWVAQKKA

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	0.81 RPM	227.19 RPM
SRP017611_kidney	0.84 RPM	364.84 RPM
SRP017611_liver	0.70 RPM	197.35 RPM
SRP040447_lung	0.40 RPM	287.27 RPM
SRP040447_skeletal_muscle	0.13 RPM	318.57 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_428 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_428 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 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009878	5 retrocopies	retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus	ENSBTAG00000002026	2 retrocopies	retro_btau_120, retro_btau_67,
Cavia porcellus	ENSCPOG00000000698	8 retrocopies	retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428 , retro_cpor_737,
Equus caballus	ENSECAG00000021065	1 retrocopy	retro_ecab_654,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Mustela putorius furo	ENSMPUG00000004150	6 retrocopies	retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Oryctolagus cuniculus	ENSOCUG00000010089	2 retrocopies	retro_ocun_265, retro_ocun_54,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pteropus vampyrus	ENSPVAG00000015117	4 retrocopies	retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus	ENSRNOG00000023529	6 retrocopies	retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Sus scrofa	ENSSSCG00000006899	2 retrocopies	retro_sscr_149, retro_sscr_219,
Tupaia belangeri	ENSTBEG00000010560	5 retrocopies	retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus	ENSTTRG00000013097	5 retrocopies	retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,