RetrogeneDB ID: retro_cpor_1355

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_71:2971521..2971916(-)
• Located in intron of: ENSCPOG00000007744

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIRC5
• Ensembl ID: ENSCPOG00000027390
• Aliases: None
• Description: baculoviral IAP repeat-containing protein 5 [Source:RefSeq peptide;Acc:NP_001186646]

Sequence

>retro_cpor_1355
TTGGGGCCCCCATTATTGTCCCAGATATAACAGCTCTACCTGAAAGAATACTGGATCTCTGTGTTCAAGAACTGGCCCTT
CTTCGATGGCCGTACCTGCACCTTGAAGCGGGTGATGGCTGAGACTGGTTTCCTCCACTGACCTGCTAAGAACAAGCCTG
ATTTGCGCAGCTCACCTTCTGCTTCATGGAGCTAGAAGGCTGGAGCAACTAGGGCAGCCCCATAGAGGAGCATAAAAAAG
CCTTCATCTGGTTTTGTGGCCTTTCTGCTAAGAAGCAGTTTAACGAATTAACTCTCAGGGAATTTTTGAAACTGGACAAA
GAGAAGGCTATGAACAAAATTGCAAAGGAAACCAATATCAAGCAGAAAGAGTTTGAAGAAAGTACAAAGAAAGTC

Alignment

ORF - retro_cpor_1355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 92.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGAPSLPRAWQLYLKEHRVSTFKNWPFVNGCSCTPER-MAEAGFIHCPTENEPDL-AQCFFCFKELEGWE
          .G.P.L....QLYLKE...S.FKNWPF..G..CT..R.MAE.GF.H.P..N.PDL.AQ..FCF.ELEGW.
Retrocopy LGPPLLSQI*QLYLKEYWISVFKNWPFFDGRTCTLKRVMAETGFLH*PAKNKPDL<AQLTFCFMELEGWS

Parental  PDDNPIEEHKKHSSGCAFLSVKKQFEELTLSEFLKLDKERAKNKIAKETNSKQKEFEETAAKV
          ....PIEEHKK.......LS.KKQF.ELTL.EFLKLDKE.A.NKIAKETN.KQKEFEE...KV
Retrocopy N*GSPIEEHKKAFIWFCGLSAKKQFNELTLREFLKLDKEKAMNKIAKETNIKQKEFEESTKKV

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	1.55 RPM
SRP017611_kidney	0.00 RPM	1.88 RPM
SRP017611_liver	0.00 RPM	1.00 RPM
SRP040447_lung	0.00 RPM	4.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.99 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1355 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1355 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027390	1 retrocopy	retro_cpor_1355 ,
Equus caballus	ENSECAG00000008466	1 retrocopy	retro_ecab_100,
Myotis lucifugus	ENSMLUG00000006281	1 retrocopy	retro_mluc_254,
Macaca mulatta	ENSMMUG00000013767	1 retrocopy	retro_mmul_19,
Monodelphis domestica	ENSMODG00000001871	2 retrocopies	retro_mdom_307, retro_mdom_996,