RetrogeneDB ID: retro_cpor_633

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:31543473..31543955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000027355
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB18
• Ensembl ID: ENSCPOG00000002234
• Aliases: None
• Description: None

Sequence

>retro_cpor_633
ATTGACCTCAAGGGGAAATTTTCAGTGGATGGAAATAAGGCTAAACTTGCAATTTGGGATACCTCCGGTCAAGAGAAGTT
TCGAACATTAACTCCCAGCTACTACAGAGGCACACAGGGTGTTACATTACATGATGATGTCACAAGAAGAGACACTTTTG
TTCAACTGGATAATTGGTTAAATGAATTGGAAGTATACAATACAAGAAATGACATAGTGAACATACTAGTTGGAAATAAA
ATCGATAAGGAAAATCATGAAGCTGATACAAATGAAGGCCTGAAATTTGCACCAAAGCATTTCATGTTTTTGATAGAGTC
AAGGGTATGTGATGGTGTACAATGTGTCTCTGAGAAACTCATTGAAAAGATCACTCAGACGCTGGACTGTGGGAGAGTGA
GAATCAGGATAAAGGAGTCAAACTGTCACACATGGAAGAGAGCCACAGAGGAAGGGCATGTGGTGATTATTGTTCTTTGT
TA

Alignment

ORF - retro_cpor_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 79.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDFKVKTISVDGNKAKLAIWWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCT
          .D.K.K..SVDGNKAKLAIW.DT.GQE.FRTLTPSYYRG.QGV.L..DVTRRDTFV.LDNWLNELE.Y.T
Retrocopy IDLKGK-FSVDGNKAKLAIW-DTSGQEKFRTLTPSYYRGTQGVTLHDDVTRRDTFVQLDNWLNELEVYNT

Parental  RNDIVNMLVGNKIDKENREVDRNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKIIQT-PGLWESEN
          RNDIVN.LVGNKIDKEN.E.D.NEGLKFA.KH.M..IE.....CDGVQC..E.L.EKI.QT..GLWESEN
Retrocopy RNDIVNILVGNKIDKENHEADTNEGLKFAPKHFMFLIE--SRVCDGVQCVSEKLIEKITQT<AGLWESEN

Parental  QNKGVKLSHMEESHGGGACGGYCSVL
          Q.KGVKLSHMEESH.G.ACG.YCS.L
Retrocopy QDKGVKLSHMEESHRGRACGDYCSLL

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	43.94 RPM
SRP017611_kidney	0.00 RPM	44.39 RPM
SRP017611_liver	0.00 RPM	39.00 RPM
SRP040447_lung	0.00 RPM	47.77 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_633 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_633 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009871	1 retrocopy	retro_btau_1691,
Choloepus hoffmanni	ENSCHOG00000005565	4 retrocopies	retro_chof_2391, retro_chof_256, retro_chof_396, retro_chof_846,
Cavia porcellus	ENSCPOG00000002234	2 retrocopies	retro_cpor_633 , retro_cpor_652,
Dipodomys ordii	ENSDORG00000014338	1 retrocopy	retro_dord_419,
Monodelphis domestica	ENSMODG00000008253	1 retrocopy	retro_mdom_146,
Oryctolagus cuniculus	ENSOCUG00000022307	2 retrocopies	retro_ocun_1699, retro_ocun_841,
Otolemur garnettii	ENSOGAG00000028015	2 retrocopies	retro_ogar_2587, retro_ogar_2973,
Rattus norvegicus	ENSRNOG00000018972	2 retrocopies	retro_rnor_2744, retro_rnor_2962,
Sarcophilus harrisii	ENSSHAG00000007613	1 retrocopy	retro_shar_281,