RetrogeneDB ID: retro_cpor_500

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:24182439..24182747(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSCPOG00000012396
• Aliases: None
• Description: None

Sequence

>retro_cpor_500
AACCCATTTTTCAGAGCTGATTTCAGAGTGTGGAAAATTACTAAAGATAAATTACACAAAATGAAAAGTCACTATATTAG
GCCACTTATTGGGAAGCCTTAGTTGGAACTACATGTATTTCAGTGGAAACTGATGACTTGAGAAAGATTACCAATCCATT
GAAAAGCAAGCACAGAGCAACAAAACAAAGCAGAAAATAAGAAGAAAGAAATAGTTACTGAAAAGGTCTAAAGGTTACCA
TGTAACGTGCTCTGGCTGATGATGGTGGTTATGACGGCAGATATGTACAGGACTATGAAGACTTCGTG

Alignment

ORF - retro_cpor_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.15 %
• Parental protein coverage: 68.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPSSRDDFTEFGKLLKDK-ITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCSEKQKQEKQS
          NP..R.DF....K..KDK.ITQ.EKSLY.A...EALV...CIS.E.DDL.KITN.L......K....KQS
Retrocopy NPFFRADFRVW-KITKDK<ITQNEKSLY*ATYWEALVGTTCISVETDDLRKITNPL----KSKHRATKQS

Parental  KAKKKKKGVVPGGGLKATMKDDLADYGGYDGGYVQDYEDFM
          ...........G..LK.TM...LAD.GGYDG.YVQDYEDF.
Retrocopy RK*EERNSY*KG--LKVTM*RALADDGGYDGRYVQDYEDFV

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	27.32 RPM
SRP017611_kidney	0.00 RPM	34.65 RPM
SRP017611_liver	0.00 RPM	31.03 RPM
SRP040447_lung	0.00 RPM	21.97 RPM
SRP040447_skeletal_muscle	0.00 RPM	36.76 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_500 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_500 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500 ,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,