RetrogeneDB ID: retro_cpor_269

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_111:3261780..3262172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAU
• Ensembl ID: ENSCPOG00000014711
• Aliases: None
• Description: None

Sequence

>retro_cpor_269
GTCATCAACATGCAGCTCTTTGTCCACACCTGGGACCTACATACCTTCAAAGTGACCAGCTAGGAAATGGTTGCCTAGAT
CAAGGCTCATGTGGCTTCACTAGAGGGCACCACACCAGAAAATCAAGTTGTGGTCTTGACAGGCAAGCCCCTGGAGGATG
AGGCCACCCTAGGCCAGTGTGGAGTGGAAGTTCAGGTCACCCTGGAAGTAACTGGCCACATGCTTGGTGGTAAAATCCAT
GGTTCCCTGCTTGAGCTGGAAAAGTGAGAGGTCAAACTCCAAAAGTGGCCAAAGAGGAGGAGGAGAAGAAGAAGACAGCC
CAGGCTAAGCAGCAGATGCAGCACAACTGGCATTTTGTCAATGTTGTGCCCATCTTTGGCAAGAAAAAGGGC

Alignment

ORF - retro_cpor_269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.24 %
• Parental protein coverage: 96.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLNMQLFVRAQDLHTLEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGKPLEDEATLGQCGVEALTTLEV
          V.NMQLFV...DLHT..VT..E.VA.IKAHVASLEG..PE.QVV.L.GKPLEDEATLGQCGVE...TLEV
Retrocopy VINMQLFVHTWDLHTFKVTS*EMVA*IKAHVASLEGTTPENQVVVLTGKPLEDEATLGQCGVEVQVTLEV

Parental  AGRMLGGKVHGSL-ARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKG
          .G.MLGGK.HGSL.A.AGKVRGQTPKVAK.E..KKKT..AK..MQ.N..FVNVVP.FGKKKG
Retrocopy TGHMLGGKIHGSL<A*AGKVRGQTPKVAKEEEEKKKTAQAKQQMQHNWHFVNVVPIFGKKKG

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	91.22 RPM
SRP017611_kidney	0.00 RPM	166.35 RPM
SRP017611_liver	0.00 RPM	164.88 RPM
SRP040447_lung	0.00 RPM	245.58 RPM
SRP040447_skeletal_muscle	0.00 RPM	185.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_269 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_269 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 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020807	1 retrocopy	retro_btau_242,
Cavia porcellus	ENSCPOG00000014711	3 retrocopies	retro_cpor_1319, retro_cpor_269 , retro_cpor_831,
Dasypus novemcinctus	ENSDNOG00000004481	5 retrocopies	retro_dnov_1406, retro_dnov_1593, retro_dnov_1651, retro_dnov_1916, retro_dnov_2021,
Monodelphis domestica	ENSMODG00000010095	1 retrocopy	retro_mdom_402,
Oryctolagus cuniculus	ENSOCUG00000014878	3 retrocopies	retro_ocun_139, retro_ocun_373, retro_ocun_939,
Sarcophilus harrisii	ENSSHAG00000000131	1 retrocopy	retro_shar_523,