RetrogeneDB ID: retro_rnor_2223

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:74925779..74926364(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000017640
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Chp
• Ensembl ID: ENSRNOG00000004742
• Aliases: Chp1, Chp, Wrch2
• Description: Calcineurin B homologous protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P61023]

Sequence

>retro_rnor_2223
ATGGGGTCTCGGGCCTCCACGTTACTGCGGGACGAAGAGCTCGAGGAGATCAAGAAGGAGACTGGCTTTTCCCACAGTCA
GATCACACGCCTGTACAGCCGCTTCACCAGCCTGGACAAAGGGGAGAACGGAACTCTCAGCCGGGAAGATTTCCAGAGGA
TTCCAGAACTTGCCATCAACCCACTGGGGGACCGGATCATCAATGCCTTCTTCTCAGAGGGAGAGGATCAGGTAAACTTC
CGAGGATTCATGAGAACTTTGGCTCATTTCCGACCCATTGAGGATAACGAAAAGAGCAAAGATGTGAATGGACTGGAACC
CCTCAACAGCCGGAGCAACAAACTGCACTTTGCTTTCAGACTTTATGACTTGGATAAAGATGACAAGATCTCCCGCGATG
AGCTGTTACAGGTACTGCGAATGATGGTCGGAGTGAATATCTCAGATGAGCAGCTGGGCAGTATTGCAGACAGGACCATC
CAGGAGGCTGACCAAGATGGAGACAGTGCCATATCTTTTACAGAATTTGTTAAGGTTTTGGAGAAGGTGGATGTAGAACA
GAAGATGAGCATCCGATTTCTTCAC

Alignment

ORF - retro_rnor_2223 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
          MGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
Retrocopy MGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF

Parental  FSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR
          FSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNG.EPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR
Retrocopy FSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGLEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR

Parental  MMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
          MMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
Retrocopy MMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH

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	0.50 RPM	39.04 RPM
SRP017611_kidney	0.14 RPM	42.78 RPM
SRP017611_liver	0.20 RPM	28.64 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2223 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223 ,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,