RetrogeneDB ID: retro_cpor_980

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:10533549..10534135(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSCPOG00000003552
• Aliases: None
• Description: None

Sequence

>retro_cpor_980
CCCAATAAACAAGAGATACAATGTCCTCTTCTTACTTCTCATCCAGGTCTACAGGGAAGAACAAAAGAAGAAACGTTCAG
GCTCTAAGGTCAATTCTGCAGAATTCTCCAAGAAATCTTTAGAGAGATGCAGGACCATGTCTCCAATGGAAAAGTTGAAA
CATGAAGATGTGGCAAAAATAACAAAGCTGCTACACAGGGAAGTAAAGAATTATGTTCCTTTCAAAGGTGATAAGAAAGG
AAAGAGAAAAGATTCCGGTGCTCCTAAAAGGATACTATTTATTTTCTTCCTGTTTTCCACTGAATATGCCCAAAGATCAA
AAGGGAACACCCAGACAGAACCATTGGAGATATTACAAAAAAATGAAGTGAAAATTAGATTGAGCAGTCAGCCAAGGATG
TACAAGCATTTGAACAGAGAGCAGCTAAACTACAGGAGAAATACAAAAAAGGTACATGGCATACCATATCAAGAGCAAAA
GTGAGGCAGGAAAAGACAGGCATGGACCACCAAGCTCAAAGAAGAATGAGGCAAAAGATAAGGTGGGGGAGACAAAGACG
AGGAGGAAGAGAATGAAGGTGAAGAA

Alignment

ORF - retro_cpor_980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.31 %
• Parental protein coverage: 95.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PNKP-RGKMSSYAF-FVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDR
          PNK..R..MSS..F...Q..REE.KKK...S.VN.AEFSKK..ER..TMS..EK.K.ED.AK..K....R
Retrocopy PNKQ<RDTMSSSYF<LIQVYREEQKKKRSGSKVNSAEFSKKSLERCRTMSPMEKLKHEDVAKITKLLH-R

Parental  EMKNYVPPKGGDKRGKKKDPNAPKRPPSAFFLFCSEHR-PKIKSEHPGLSIGDTAKKLGEMWSEQSAKDK
          E.KNYVP.KG.DK.GK.KD..APKR....FFLF..E...PKIK.EHP...IGD..KK..E...EQSAKD.
Retrocopy EVKNYVPFKG-DKKGKRKDSGAPKRILFIFFLFSTEYA<PKIKREHPDRTIGDITKK*SEN*IEQSAKDV

Parental  QPYEQKAAKLKEKY-EKDIAAYRAKGKSEAGKKGPGRPTGSKKKNEPEDEEEE-EEEEEEEEEEEE
          Q..EQ.AAKL.EKY..K...AY..K.KSEAGK...G.P..S.KKNE..D...E....EEEE.E.EE
Retrocopy QAFEQRAAKLQEKY<QKRYMAYHIKSKSEAGKDRHGPP--SSKKNEAKDKVGE<DKDEEEENEGEE

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	6.67 RPM
SRP017611_kidney	0.00 RPM	16.96 RPM
SRP017611_liver	0.00 RPM	9.10 RPM
SRP040447_lung	0.05 RPM	25.90 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.04 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_980 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_980 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 18 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Cavia porcellus	ENSCPOG00000000601	2 retrocopies	retro_cpor_1432, retro_cpor_384,
Cavia porcellus	ENSCPOG00000003552	4 retrocopies	retro_cpor_1100, retro_cpor_604, retro_cpor_890, retro_cpor_980 ,
Cavia porcellus	ENSCPOG00000003985	1 retrocopy	retro_cpor_69,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Erinaceus europaeus	ENSEEUG00000012238	8 retrocopies	retro_eeur_118, retro_eeur_223, retro_eeur_345, retro_eeur_49, retro_eeur_54, retro_eeur_661, retro_eeur_702, retro_eeur_86,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,