RetrogeneDB ID: retro_sscr_515

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:155554202..155554661(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016386
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHCHD2
• Ensembl ID: ENSSSCG00000007743
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 2 [Source:HGNC Symbol;Acc:21645]

Sequence

>retro_sscr_515
ATGCCTCGTGGAAGCCGAAGCCGCAGTTTCCACATGGCCCCTCCGGCTAGCCGGGCACCTCAGATGAGAGCTGCACCCAG
GCCAGCGCTGGCAGCTCAGCCACCAGCAGCAGCTCCACCATCTGCTGTTGGCTCCCCTGCTGCTGCACCTCGGCAGCCAG
GTCTCATGGCCCAGATGGCAACCACTGTAGCCGGCGTGGCTGTGGGTTCTGCCGTCGGCCACACGATAGGTCATGCGATC
ACTGGGGGCTTCGGTGGAGGAAGTAGTGCTGAGCCCTCAAGGCCTGACATCACTTACCAGGAGCCTCAGGGAGCCCAGCC
AGCACAGCAGCAGCAGATTGGCCCATGCTTCTATGAGGTGAAACAGTTTTTGGAGTGTGCCCAGAACCAGGGTGACCTTA
AGCTTTGTGAGGGTTTCAGCGAGGTGTTGAAACAATGCAGACTGGCAAATGGATTATCT

Alignment

ORF - retro_sscr_515 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRGSRSRTSRMAPPASRAPQMRAAPRPAPAAQPPAAAPPSAVGSPAAAPRQPGLMAQMATTAAGVAVGS
          MPRGSRSR...MAPPASRAPQMRAAPRPA.AAQPPAAAPPSAVGSPAAAPRQPGLMAQMATT.AGVAVGS
Retrocopy MPRGSRSRSFHMAPPASRAPQMRAAPRPALAAQPPAAAPPSAVGSPAAAPRQPGLMAQMATTVAGVAVGS

Parental  AVGHTIGHAITGGFGGGSSAEPSRPDITYQEPQGAQPAQQQQMAPCFYEVKQFLECAQNQGDLKLCEGFS
          AVGHTIGHAITGGFGGGSSAEPSRPDITYQEPQGAQPAQQQQ..PCFYEVKQFLECAQNQGDLKLCEGFS
Retrocopy AVGHTIGHAITGGFGGGSSAEPSRPDITYQEPQGAQPAQQQQIGPCFYEVKQFLECAQNQGDLKLCEGFS

Parental  EVLKQCRLANGLS
          EVLKQCRLANGLS
Retrocopy EVLKQCRLANGLS

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	0.93 RPM	173.61 RPM
SRP014902_testis	0.42 RPM	75.82 RPM
SRP018288_heart	2.23 RPM	108.83 RPM
SRP018288_kidney	6.30 RPM	266.65 RPM
SRP018288_liver	4.00 RPM	157.35 RPM
SRP018288_lung	0.51 RPM	93.07 RPM
SRP018856_adipose	0.52 RPM	96.38 RPM
SRP035408_brain	0.95 RPM	80.26 RPM
SRP035408_liver	2.55 RPM	99.05 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_515 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_515 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016050	2 retrocopies	retro_amel_500, retro_amel_976,
Bos taurus	ENSBTAG00000040295	2 retrocopies	retro_btau_397, retro_btau_768,
Canis familiaris	ENSCAFG00000010178	1 retrocopy	retro_cfam_1653,
Callithrix jacchus	ENSCJAG00000021267	1 retrocopy	retro_cjac_271,
Erinaceus europaeus	ENSEEUG00000012857	1 retrocopy	retro_eeur_398,
Echinops telfairi	ENSETEG00000008598	1 retrocopy	retro_etel_45,
Homo sapiens	ENSG00000106153	8 retrocopies	retro_hsap_116, retro_hsap_1180, retro_hsap_1995, retro_hsap_3063, retro_hsap_3186, retro_hsap_4057, retro_hsap_4184, retro_hsap_4752,
Gorilla gorilla	ENSGGOG00000014938	8 retrocopies	retro_ggor_2103, retro_ggor_220, retro_ggor_2725, retro_ggor_2807, retro_ggor_2808, retro_ggor_2958, retro_ggor_918, retro_ggor_989,
Myotis lucifugus	ENSMLUG00000015151	1 retrocopy	retro_mluc_345,
Macaca mulatta	ENSMMUG00000015278	2 retrocopies	retro_mmul_160, retro_mmul_302,
Mus musculus	ENSMUSG00000070493	2 retrocopies	retro_mmus_2340, retro_mmus_2536,
Nomascus leucogenys	ENSNLEG00000015819	6 retrocopies	retro_nleu_1250, retro_nleu_1657, retro_nleu_2096, retro_nleu_2108, retro_nleu_555, retro_nleu_770,
Otolemur garnettii	ENSOGAG00000010097	5 retrocopies	retro_ogar_1161, retro_ogar_158, retro_ogar_1848, retro_ogar_2837, retro_ogar_34,
Pongo abelii	ENSPPYG00000017543	4 retrocopies	retro_pabe_131, retro_pabe_139, retro_pabe_1755, retro_pabe_496,
Pan troglodytes	ENSPTRG00000019209	9 retrocopies	retro_ptro_129, retro_ptro_1331, retro_ptro_2065, retro_ptro_2259, retro_ptro_2750, retro_ptro_2838, retro_ptro_3046, retro_ptro_3167, retro_ptro_809,
Sus scrofa	ENSSSCG00000007743	1 retrocopy	retro_sscr_515 ,
Ictidomys tridecemlineatus	ENSSTOG00000010512	3 retrocopies	retro_itri_1870, retro_itri_670, retro_itri_671,
Tupaia belangeri	ENSTBEG00000012905	15 retrocopies	retro_tbel_1728, retro_tbel_1891, retro_tbel_2513, retro_tbel_2593, retro_tbel_2596, retro_tbel_2658, retro_tbel_3331, retro_tbel_3764, retro_tbel_3777, retro_tbel_3954, retro_tbel_4082, retro_tbel_4368, retro_tbel_4487, retro_tbel_4728, retro_tbel_817,
Tursiops truncatus	ENSTTRG00000015185	1 retrocopy	retro_ttru_520,
Vicugna pacos	ENSVPAG00000006104	1 retrocopy	retro_vpac_48,