RetrogeneDB ID: retro_cpor_1028

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:10996649..10997021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSCPOG00000014169
• Aliases: None
• Description: None

Sequence

>retro_cpor_1028
AAGCTAGCACAACTTGCCTATTTCAATGATATTGCTGTTGGTGCAGTGTGCTGCAGGGTGGGTCATTCACAGATTCAGAA
GAGACTTTACATCATGACACTAGGAGGTCTTGCAACCTTACTGAAGGCTAGAAATAGGAACTAAAGTGTTAAATCATGTC
TTAAACATCTGTGAGAAAGATGGCACTTTGGGCAATATCTATCTGTATGTCCAGATCAGCAATGAGGCGGCGATTGACTT
CTACAGGAAATTTGACTTTGAGATTATTAAAACAAAGAGCTACTAGAAGAGGATAGAGCCTGCTGATGCTCACGTGCTTC
TGAAAAATCTCAGTGTGCTTCTGGTCAGTATGCAGATGTGCAAAAGACAGAC

Alignment

ORF - retro_cpor_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 73.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLA-PYRRLGIGTKMLNHVLNICEKDGTFDNIYLH
          .LA.LAYFNDIAVGAVCCRV.HSQ.QKRLYIMTLG.LA.PY.RL.IGTK.LNHVLNICEKDGT..NIYL.
Retrocopy KLAQLAYFNDIAVGAVCCRVGHSQIQKRLYIMTLGGLA>PY*RLEIGTKVLNHVLNICEKDGTLGNIYLY

Parental  VQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKV-PSGQNADAQKTD
          VQISNE.AIDFYRKF.FEII.T.K.Y.KRIEPADAHVL.KNL.V..SGQ.AD.QKTD
Retrocopy VQISNEAAIDFYRKFDFEIIKT-KSY*KRIEPADAHVLLKNLSV<ASGQYADVQKTD

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	17.02 RPM
SRP017611_kidney	0.00 RPM	23.87 RPM
SRP017611_liver	0.00 RPM	29.73 RPM
SRP040447_lung	0.00 RPM	26.71 RPM
SRP040447_skeletal_muscle	0.00 RPM	82.56 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1028 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1028 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 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014169	6 retrocopies	retro_cpor_1027, retro_cpor_1028 , retro_cpor_1199, retro_cpor_1200, retro_cpor_217, retro_cpor_480,
Gorilla gorilla	ENSGGOG00000006589	2 retrocopies	retro_ggor_432, retro_ggor_710,
Loxodonta africana	ENSLAFG00000004023	1 retrocopy	retro_lafr_1159,
Oryctolagus cuniculus	ENSOCUG00000006467	2 retrocopies	retro_ocun_466, retro_ocun_984,
Otolemur garnettii	ENSOGAG00000011197	1 retrocopy	retro_ogar_157,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,