RetrogeneDB ID: retro_sscr_297

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:53946134..53946409(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA3
• Ensembl ID: ENSSSCG00000023886
• Aliases: None
• Description: replication protein A3, 14kDa [Source:HGNC Symbol;Acc:10291]

Sequence

>retro_sscr_297
AGGCTGGAGAAGATGCATCCCACTGGAAAATGTTTATTCTTTCAGATGGAAAAGGAAAAAGTGTAACCACTGAATTGGTG
CAGCCTCTTGATGAAGAAATCTCTGGAATCGTGGAAGTGGTTGGAAGAGTCACAACCAAGGCAACCATTATGTGTGCCTC
CTACATCCAGTGTAAAGAAGATAACCATCCTTTTGATCTTGGACTTTAATATAACGAAGCTGTGGAAATTACCCATGAGT
TCCCTCAGTGTTTTCCTTTGGGCGTTGTGCAGCAT

Alignment

ORF - retro_sscr_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 75.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLEKIHPTGK-MFILSDGEGKNVTIELMEPLDEEISGIVEVVGRVTGKATIMCVSYIQFKEDNHPFDLGL
          RLEK.HPTGK.MFILSDG.GK.VT.EL..PLDEEISGIVEVVGRVT.KATIMC.SYIQ.KEDNHPFDLGL
Retrocopy RLEKMHPTGK<MFILSDGKGKSVTTELVQPLDEEISGIVEVVGRVTTKATIMCASYIQCKEDNHPFDLGL

Parental  -YNEAVKIIHEFPQYFPLGVVQH
          .YNEAV.I.HEFPQ.FPLGVVQH
Retrocopy *YNEAVEITHEFPQCFPLGVVQH

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	1.06 RPM
SRP014902_testis	0.00 RPM	9.90 RPM
SRP018288_heart	0.00 RPM	5.76 RPM
SRP018288_kidney	0.00 RPM	14.68 RPM
SRP018288_liver	0.00 RPM	11.99 RPM
SRP018288_lung	0.00 RPM	4.79 RPM
SRP018856_adipose	0.00 RPM	13.15 RPM
SRP035408_brain	0.00 RPM	11.47 RPM
SRP035408_liver	0.00 RPM	17.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_297 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_297 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016401	1 retrocopy	retro_amel_1031,
Callithrix jacchus	ENSCJAG00000000705	1 retrocopy	retro_cjac_3111,
Cavia porcellus	ENSCPOG00000011748	2 retrocopies	retro_cpor_855, retro_cpor_998,
Dasypus novemcinctus	ENSDNOG00000011718	3 retrocopies	retro_dnov_1044, retro_dnov_1824, retro_dnov_2045,
Equus caballus	ENSECAG00000007680	2 retrocopies	retro_ecab_212, retro_ecab_819,
Felis catus	ENSFCAG00000025369	1 retrocopy	retro_fcat_1287,
Homo sapiens	ENSG00000106399	2 retrocopies	retro_hsap_2179, retro_hsap_3473,
Gorilla gorilla	ENSGGOG00000022464	2 retrocopies	retro_ggor_1727, retro_ggor_2342,
Microcebus murinus	ENSMICG00000000741	1 retrocopy	retro_mmur_934,
Myotis lucifugus	ENSMLUG00000007421	1 retrocopy	retro_mluc_852,
Macaca mulatta	ENSMMUG00000000854	2 retrocopies	retro_mmul_131, retro_mmul_909,
Mus musculus	ENSMUSG00000012483	1 retrocopy	retro_mmus_413,
Nomascus leucogenys	ENSNLEG00000016151	2 retrocopies	retro_nleu_308, retro_nleu_340,
Oryctolagus cuniculus	ENSOCUG00000000467	1 retrocopy	retro_ocun_1097,
Otolemur garnettii	ENSOGAG00000001018	1 retrocopy	retro_ogar_113,
Pongo abelii	ENSPPYG00000017787	2 retrocopies	retro_pabe_2062, retro_pabe_2868,
Pan troglodytes	ENSPTRG00000018927	1 retrocopy	retro_ptro_2354,
Rattus norvegicus	ENSRNOG00000008309	2 retrocopies	retro_rnor_2803, retro_rnor_53,
Sus scrofa	ENSSSCG00000023886	1 retrocopy	retro_sscr_297 ,
Tupaia belangeri	ENSTBEG00000010930	6 retrocopies	retro_tbel_1347, retro_tbel_1876, retro_tbel_2736, retro_tbel_4029, retro_tbel_87, retro_tbel_917,