RetrogeneDB ID: retro_cpor_465

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:15644667..15645117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFDP1
• Ensembl ID: ENSCPOG00000000695
• Aliases: None
• Description: None

Sequence

>retro_cpor_465
AAAGTGCCCCCAGTACACAGGCACAGAGGAAAACAGGCTGAAGAGAGGAGTCAAAAACCCTTGGTCAAAGCAGAAGGGCC
AGAGAAACCTAAAGAAGTAGAAAGGGTTACAGTCTCTAAGAAGATCGAAGGAAAGGAGACTGAGGCGGTGGATGCTGCAT
CTAAAGAAGCCAAATCCTTCTTCATGCAAAACGAGAAAGGAGAACCACAGCCCAGTGCCCCTTCTGCCAGCTGTGCAGTC
ACTGTCTGCTGGACCAGTGTTAAAAAGTCAAGTGGCATGAGCAGCCTTTGGGGGAGCATGGGAGCCAAGAAGCAGAAAAT
GCGCACTCTTGAGAAGTCCAAATTGGGCTGGGAGAGCTTCCAGGAGGAAGAAGGAGTTGGCGAAGAACTGGCTGTCCATA
ATGGAGGGAAAGAAGGGTACATGGAACGGAAAGCGTTTCTGGAGAGTGTG

Alignment

ORF - retro_cpor_465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.62 %
• Parental protein coverage: 52.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVPPSTQAKTEEQTEETTSSKSLIKTEELEKPKEAEKVKITKVFDFAGEEVRVTKEVDATSKEAKSFFKQ
          KVPP..........E...S.K.L.K.E..EKPK..E....T......G.E...T..VDA.SKEAKSFF.Q
Retrocopy KVPPVHRHRGKQAEER--SQKPLVKAEGPEKPK--EVERVTVSKKIEGKE---TEAVDAASKEAKSFFMQ

Parental  NE-KEKPQSSAPL--AAPSLSAGPGLK-RSSGMSSLLGKIGAKKQKMSTLEKSKLDWESFKEEEGIGEEL
          NE.KE...S..PL..A..SLSAGP.LK..SSGMSSL.G..GAKKQKM.TLEKSKL.WESF.EEEG.GEEL
Retrocopy NE>KEN-HSPVPLLPAVQSLSAGPVLK<KSSGMSSLWGSMGAKKQKMRTLEKSKLGWESFQEEEGVGEEL

Parental  AIHNRGKEGYIERKAFLERV
          A.HN.GKEGY.ERKAFLE.V
Retrocopy AVHNGGKEGYMERKAFLESV

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	27.03 RPM
SRP017611_kidney	0.00 RPM	40.93 RPM
SRP017611_liver	0.00 RPM	33.69 RPM
SRP040447_lung	0.00 RPM	30.97 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_465 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_465 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465 ,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117, retro_itri_1815,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385,