RetrogeneDB ID: retro_cpor_1357

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_71:4453030..4453347(-)
• 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_1357
CAAGACATGATTTCACAGTTTGTCAAGTTACTAAAAAATAAAATTAGGCAGTATAAAAAGTCACTGTATTATGCCAGCTT
TTTGGAGGGAAGCTATGAGATGTGTGTATTTGATTGAAAACTGATGACTTGAAAAAGATTACGAATTCATTGTCTGTGCT
TTGCTGTTGGAAACAGAAGTAAGCAAAGCAAAGCAAAACCAAAAAGGAGAAGAAAGGTGTGGTTCCTGGAGGGACATTAA
AGGCTACCATGAAAGACAGTCTGGCAGATTATGGAGGTTATCATGAAGGATATGCACAAGACCATGAAGACTTCATG

Alignment

ORF - retro_cpor_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.96 %
• Parental protein coverage: 66.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDDFTEFGKLLKDKITQYEKSLYYASFLEALVR-DVCISLEIDDLKKITNSLTVLCSEKQKQEKQSKAKK
          .D....F.KLLK.KI.QY.KSLYYASFLE.....DVCI.L..DDLKKITNSL.VLC..KQK..KQSK.KK
Retrocopy QDMISQFVKLLKNKIRQYKKSLYYASFLEGSYE<DVCI*LKTDDLKKITNSLSVLCCWKQK*AKQSKTKK

Parental  KKKGVVPGGGLKATMKDDLADYGGYDGGYVQDYEDFM
          .KKGVVPGG.LKATMKD.LADYGGY..GY.QD.EDFM
Retrocopy EKKGVVPGGTLKATMKDSLADYGGYHEGYAQDHEDFM

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_1357 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1357 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.

---

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,