RetrogeneDB ID: retro_sscr_407

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:21197455..21197914(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000009710
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NHP2
• Ensembl ID: ENSSSCG00000014032
• Aliases: None
• Description: NHP2 ribonucleoprotein [Source:HGNC Symbol;Acc:14377]

Sequence

>retro_sscr_407
ATGACCAAAATAAAGGCAGATCCCAACAGGCCAGAGGCTCAGACAGAAGCATGCTGTGGGGAGCATGCTTACCATGAACT
GCTGGTGAAATCTGAACCCCACTGTGCACCCCCTGGCTTCTCGCAGACTTACAGGGAAGCTCTACAAATGCATCAAGAAA
GCCATAAAGCAGAAGCAGATTCAGCGCGGGGTGAAGGAGGTTCAGAAATTTATCAACAAAGGCGAGAAAGGGATCATGGT
TTTGGCAGGAGACACGTTACTGGTTGAGGTATACTGCCATCTCCCAGTTATGTGTGAAGACCAGAATTTGCCCTACATCT
ATATCCCCTCTAAGACAACCTGGGTGCAGCTGCTGGCTCCAAGCGCCCCACCTGTGTGATAATGGTCAAGTCCCATAAGG
AATACCAGGAAGCCTATGACGAGTGCCTGGAGGAGGTGCAAGCCCTGCCCCCACCCATG

Alignment

ORF - retro_sscr_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTKIKADPDGPEAQADACCGERTYHELLV-NLNPIAQPLASRKLTRKLYKCIIAAVKQKQIRRGVKEVQK
          MTKIKADP..PEAQ..ACCGE..YHELLV.NLNP...PLASR.LT.KLYKCI..A.KQKQI.RGVKEVQK
Retrocopy MTKIKADPNRPEAQTEACCGEHAYHELLV>NLNPTVHPLASRRLTGKLYKCIKKAIKQKQIQRGVKEVQK

Parental  FINKGEKGIMVLAGDTLPVEVYCHLPVMCEDRNLPYVYIPSKT-DLGAAAGSKRPTCVIMVKPHEEYQEA
          FINKGEKGIMVLAGDTL.VEVYCHLPVMCED.NLPY.YIPSKT..LGAAAGSKRPTCVIMVK.H.EYQEA
Retrocopy FINKGEKGIMVLAGDTLLVEVYCHLPVMCEDQNLPYIYIPSKT<NLGAAAGSKRPTCVIMVKSHKEYQEA

Parental  YDECLEEVQALPPPM
          YDECLEEVQALPPPM
Retrocopy YDECLEEVQALPPPM

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
SRP014902_placenta	0.00 RPM	3.72 RPM
SRP014902_testis	0.00 RPM	8.20 RPM
SRP018288_heart	0.03 RPM	7.28 RPM
SRP018288_kidney	0.00 RPM	7.98 RPM
SRP018288_liver	0.16 RPM	11.51 RPM
SRP018288_lung	0.00 RPM	4.99 RPM
SRP018856_adipose	0.00 RPM	5.82 RPM
SRP035408_brain	0.13 RPM	9.85 RPM
SRP035408_liver	0.12 RPM	9.36 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_407 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_407 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407 ,