RetrogeneDB ID: retro_cpor_707

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:16050884..16051346(-)
• Located in intron of: ENSCPOG00000010051

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50A
• Ensembl ID: ENSCPOG00000012615
• Aliases: None
• Description: None

Sequence

>retro_cpor_707
TCTGGATTTCTAGAAGGTACGAGATGTTCCCAATGCATTGACAGGAGGAAAAAGCACAATACTATTGCTTCCATCCCTAC
TGGTGGTGTTTTTCACAGGCGGGTGGATTATTGTAAATACAACTGTTATTTATCTCAGTATCGAAGAGTTCAACCACTAA
TACCATGCCTATGGCATTAAAGCAACCATAACCTTCCTAATGAGTAATGCAGTATTATAGGACAAGCCTAGGGTGCCAGT
TATAGTGAAGACTGAGTCAAACAGGTACTAGCATTTGGTTCTTCACTGGGTTTCACGCTGGCCTTTGGATCTCTGATTGT
GTCTAATTGGATTTTCTTTGGAGGTTATATTGGCAAGAAAAAAACAATAGTATATTTTGGCATTGCTGTATTTTTCCAGA
ATGCATTTGTATTTTCTGTAGGACTAGTGTTTAAGTTTGGCCCCATGGAAGACTTGTAGCAA

Alignment

ORF - retro_cpor_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.76 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGFLEGMRCSECIDWGEKRNTIASIAAG-ILFFTGWWIIIDAAVNYPKMEDFNHSYHACGVIATIAFLMI
          SGFLEG.RCS.CID...K.NTIASI..G...F..G.WII....V.Y...E.FNH.YHA.G..ATI.FLM.
Retrocopy SGFLEGTRCSQCIDRRKKHNTIASIPTG>VFFTGG-WIIVNTTVIYLSIEEFNH*YHAYGIKATITFLMS

Parental  NAV-SNGQVRGDSYSEGCLGQTGARIWLFIGFMLAFGSLIASMWILFGGYVAKEKPIVYPGIAVFFQNAF
          NAV...GQ..G.SYSE....Q..A......GF.LAFGSLI.S.WI.FGGY..K.K.IVY.GIAVFFQNAF
Retrocopy NAV<IIGQA*GASYSED*VKQVLA-FGSSLGFTLAFGSLIVSNWIFFGGYIGKKKTIVYFGIAVFFQNAF

Parental  IFFGGLVFKFGRTEDLWQ
          .F..GLVFKFG..EDL.Q
Retrocopy VFSVGLVFKFGPMEDL*Q

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	0.23 RPM	21.28 RPM
SRP017611_kidney	0.21 RPM	28.06 RPM
SRP017611_liver	0.04 RPM	21.42 RPM
SRP040447_lung	0.15 RPM	50.42 RPM
SRP040447_skeletal_muscle	0.04 RPM	14.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_707 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_707 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018575	1 retrocopy	retro_cjac_1677,
Cavia porcellus	ENSCPOG00000012615	1 retrocopy	retro_cpor_707 ,
Echinops telfairi	ENSETEG00000007483	1 retrocopy	retro_etel_2061,
Macropus eugenii	ENSMEUG00000002060	1 retrocopy	retro_meug_1270,
Macaca mulatta	ENSMMUG00000032217	1 retrocopy	retro_mmul_1408,
Ochotona princeps	ENSOPRG00000001182	2 retrocopies	retro_opri_546, retro_opri_62,
Pongo abelii	ENSPPYG00000001711	1 retrocopy	retro_pabe_1679,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329,