RetrogeneDB ID: retro_cpor_1542

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:5510926..5511346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THYN1
• Ensembl ID: ENSCPOG00000006567
• Aliases: None
• Description: None

Sequence

>retro_cpor_1542
CAGCCCAAGCAAATAGCCTGCTGGGCGGTGTTTGAAACAACCAGCCTTGTAACTTCTTTGGAGCCATGGAGCTGGAGCAT
GAAGCCTTCTTCTATCATAGTAACTGCAAGGAGCCAGGCATCACAGCACTTACGAAGACTGCAAAGGAGGCTGACACAGA
CCACACACAATTTGAGAAAAACAGTCCCCATTGTGACCCACACAATGAAAAGAACAACCCCCAGTGGCTCATGGTGGATG
TACAGTTGCTCAGATAATGAAGCATTTCACCTCCCTGGCTGAGCTTCAGATCTATCACTGAGCTCACAAAGCTACTGGTG
GTCCATTAAAGAAACGTGGCCCTCTTCACTTGCCAGACTCTCGATTCAGCTCCTTACCCAAGAAGAATTCAGTTTTATTT
TGAGCCTCAAAGAAAAGGAA

Alignment

ORF - retro_cpor_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.19 %
• Parental protein coverage: 67.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EPEQTACW-DGVRNYQARNFLRAMKLEDEAFFYHSNCKEPGIAGLVKIVKEAYPDHTQFEKNSPHYDPSS
          .P.Q.ACW..GV.N.Q..NF..AM.LE.EAFFYHSNCKEPGI..L.K..KEA..DHTQFEKNSPH.DP..
Retrocopy QPKQIACW<GGV*NNQPCNFFGAMELEHEAFFYHSNCKEPGITALTKTAKEADTDHTQFEKNSPHCDPHN

Parental  KKDNPKWFMVDVQLVR-KLKRFISLAELKTYHQAHKTSDGP-LKNMALFTRQRLSIQSLTQEEFDFILHL
          .K.NP.W.MVDVQL.R...K.F.SLAEL..YH.AHK...GP..K........RLSIQ.LTQEEF.FIL.L
Retrocopy EKNNPQWLMVDVQLLR<IMKHFTSLAELQIYH*AHKATGGP<IKETWPSSLARLSIQLLTQEEFSFILSL

Parental  EEKE
          .EKE
Retrocopy KEKE

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	6.10 RPM
SRP017611_kidney	0.00 RPM	12.25 RPM
SRP017611_liver	0.00 RPM	13.23 RPM
SRP040447_lung	0.00 RPM	9.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1542 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1542 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007294	1 retrocopy	retro_amel_300,
Canis familiaris	ENSCAFG00000009772	1 retrocopy	retro_cfam_877,
Cavia porcellus	ENSCPOG00000006567	1 retrocopy	retro_cpor_1542 ,
Felis catus	ENSFCAG00000007419	1 retrocopy	retro_fcat_946,
Macropus eugenii	ENSMEUG00000008297	1 retrocopy	retro_meug_287,
Mustela putorius furo	ENSMPUG00000009185	1 retrocopy	retro_mputfur_1114,