RetrogeneDB ID: retro_sscr_152

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:32397699..32398064(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H2AFV
• Ensembl ID: ENSSSCG00000016738
• Aliases: None
• Description: H2A histone family, member V [Source:HGNC Symbol;Acc:20664]

Sequence

>retro_sscr_152
AAGGCTTGGAAGGACTTTGGAAAGTCCAAGACAAAGGCGGGTTCCCGCTCTCAGAGAGCAAGTTTGCAGTTTCCTGTGGG
CCATATTCATTGACCTCTGAAATCTCAGACGACCAGCCATGGATGCATGGGTGCGACTGCCTCTGTGTACAGTGCAGACA
TCCTGAAGAACATCACTCCAGAGGTATTTGAATTGGCAGGAAACGCATCAAAAAATCTGAAGGTAATGTGTATTACTCCT
CATCACTTGCAACTGGCTATTCGTGGGAAAGTGTTGGATTATCTCATCAAGGCTACAGTTGCTGGTGGTGGTGTCATTCC
ACACATCCACAAATCTCTGGGGAGAAAGGACAACAGAAGTCTGCC

Alignment

ORF - retro_sscr_152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.6 %
• Parental protein coverage: 97.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAGKDSGKAKAKAVSRSQRAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNAS
          KA.KD.GK.K.KA.SRSQRA.LQFPVG.IH..LK..TTSHG..GATA.VYSA.IL...T.EV.ELAGNAS
Retrocopy KAWKDFGKSKTKAGSRSQRASLQFPVGHIH*PLKSQTTSHGCMGATASVYSADILKNITPEVFELAGNAS

Parental  KDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGK-KGQQKTA
          K.LKV..ITP.HLQLAIRG...LD.LIKAT.AGGGVIPHIHKSL.G..KGQQK.A
Retrocopy KNLKVMCITPHHLQLAIRG-KVLDYLIKATVAGGGVIPHIHKSL-GR<KGQQKSA

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	58.14 RPM
SRP014902_testis	0.00 RPM	111.04 RPM
SRP018288_heart	0.00 RPM	52.91 RPM
SRP018288_kidney	0.00 RPM	140.57 RPM
SRP018288_liver	0.00 RPM	57.25 RPM
SRP018288_lung	0.00 RPM	39.92 RPM
SRP018856_adipose	0.00 RPM	76.61 RPM
SRP035408_brain	0.00 RPM	19.63 RPM
SRP035408_liver	0.00 RPM	49.02 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_152 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000889	3 retrocopies	retro_chof_1967, retro_chof_2205, retro_chof_576,
Callithrix jacchus	ENSCJAG00000011953	1 retrocopy	retro_cjac_3029,
Cavia porcellus	ENSCPOG00000000769	1 retrocopy	retro_cpor_37,
Dipodomys ordii	ENSDORG00000000793	5 retrocopies	retro_dord_100, retro_dord_12, retro_dord_171, retro_dord_195, retro_dord_291,
Homo sapiens	ENSG00000105968	2 retrocopies	retro_hsap_1612, retro_hsap_890,
Myotis lucifugus	ENSMLUG00000014500	2 retrocopies	retro_mluc_1492, retro_mluc_2122,
Mus musculus	ENSMUSG00000041126	2 retrocopies	retro_mmus_1229, retro_mmus_1481,
Ornithorhynchus anatinus	ENSOANG00000009378	2 retrocopies	retro_oana_55, retro_oana_87,
Oryctolagus cuniculus	ENSOCUG00000008133	10 retrocopies	retro_ocun_1226, retro_ocun_1336, retro_ocun_1456, retro_ocun_1596, retro_ocun_1938, retro_ocun_385, retro_ocun_389, retro_ocun_523, retro_ocun_601, retro_ocun_778,
Otolemur garnettii	ENSOGAG00000025145	1 retrocopy	retro_ogar_3181,
Ochotona princeps	ENSOPRG00000015604	3 retrocopies	retro_opri_315, retro_opri_538, retro_opri_942,
Pelodiscus sinensis	ENSPSIG00000005931	1 retrocopy	retro_psin_62,
Pan troglodytes	ENSPTRG00000019153	1 retrocopy	retro_ptro_1081,
Rattus norvegicus	ENSRNOG00000007026	5 retrocopies	retro_rnor_1410, retro_rnor_1815, retro_rnor_1935, retro_rnor_2102, retro_rnor_2310,
Sus scrofa	ENSSSCG00000016738	1 retrocopy	retro_sscr_152 ,
Ictidomys tridecemlineatus	ENSSTOG00000011533	1 retrocopy	retro_itri_148,
Tupaia belangeri	ENSTBEG00000013840	5 retrocopies	retro_tbel_1155, retro_tbel_1295, retro_tbel_2747, retro_tbel_3214, retro_tbel_970,
Vicugna pacos	ENSVPAG00000004507	1 retrocopy	retro_vpac_608,