RetrogeneDB ID: retro_sscr_834

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:38031844..38032127(+)
• Located in intron of: ENSSSCG00000002859

Retrocopy information

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

Parental gene information

• Parental gene symbol: HRSP12
• Ensembl ID: ENSSSCG00000006079
• Aliases: None
• Description: heat-responsive protein 12 [Source:HGNC Symbol;Acc:16897]

Sequence

>retro_sscr_834
ATGTCATCCTTGATCAGAAAGGTGATCAGCACAGAGAAAGCCTCAAGGCCACTGGTCCTCAAATCAAGCTGTGTTAGTGG
ACAGGGTCACTTACATTTCAAGACAACAAGGCACAGACCCTTTAAGGGGACAGCTTTTTGCAGGAGGGGTGATGGAAGAG
GCTAAACAAGCCTTAGAAACAGGTGAAACTCTGAAGGCGGCAGGCTGTGACCTCATGACTGTGGTCGAAACAGCTGTGCT
GCTGGCTGCTGTGGATGACTTCAGTCCTGTCAGTGAAATCCAC

Alignment

ORF - retro_sscr_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSALVRKVISTVKAPA-AIGPY-SQAVLVDRTIYISGQIGMDPASGQLVPGGVVEEAKQALTNMGEILKA
          MS.L.RKVIST.KA...A.GP...QAVLVDR..YIS.Q.G.DP..GQL..GGV.EEAKQAL...GE.LKA
Retrocopy MSSLIRKVISTEKASR<ATGPQ<NQAVLVDRVTYISRQQGTDPLRGQLFAGGVMEEAKQAL-ETGETLKA

Parental  AGCDFTNVVKTTVLLADINDFSTVNDIY
          AGCD...VV.T.VLLA...DFS.V..I.
Retrocopy AGCDLMTVVETAVLLAAVDDFSPVSEIH

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	7.30 RPM
SRP014902_testis	0.00 RPM	7.21 RPM
SRP018288_heart	0.00 RPM	15.04 RPM
SRP018288_kidney	0.00 RPM	383.97 RPM
SRP018288_liver	0.00 RPM	317.26 RPM
SRP018288_lung	0.00 RPM	26.37 RPM
SRP018856_adipose	0.00 RPM	36.70 RPM
SRP035408_brain	0.00 RPM	65.08 RPM
SRP035408_liver	0.00 RPM	630.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_834 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000575	1 retrocopy	retro_amel_1033,
Bos taurus	ENSBTAG00000012595	5 retrocopies	retro_btau_1068, retro_btau_1145, retro_btau_1328, retro_btau_771, retro_btau_912,
Canis familiaris	ENSCAFG00000030250	1 retrocopy	retro_cfam_668,
Choloepus hoffmanni	ENSCHOG00000001278	8 retrocopies	retro_chof_133, retro_chof_1972, retro_chof_2434, retro_chof_2503, retro_chof_2676, retro_chof_380, retro_chof_515, retro_chof_757,
Callithrix jacchus	ENSCJAG00000015560	2 retrocopies	retro_cjac_1702, retro_cjac_465,
Dasypus novemcinctus	ENSDNOG00000025138	3 retrocopies	retro_dnov_1155, retro_dnov_224, retro_dnov_793,
Felis catus	ENSFCAG00000002167	1 retrocopy	retro_fcat_624,
Homo sapiens	ENSG00000132541	3 retrocopies	retro_hsap_1502, retro_hsap_284, retro_hsap_3022,
Gorilla gorilla	ENSGGOG00000001185	1 retrocopy	retro_ggor_1153,
Loxodonta africana	ENSLAFG00000002078	1 retrocopy	retro_lafr_437,
Microcebus murinus	ENSMICG00000004356	13 retrocopies	retro_mmur_1096, retro_mmur_1206, retro_mmur_1323, retro_mmur_209, retro_mmur_222, retro_mmur_364, retro_mmur_533, retro_mmur_589, retro_mmur_597, retro_mmur_603, retro_mmur_79, retro_mmur_870, retro_mmur_97,
Macaca mulatta	ENSMMUG00000011825	2 retrocopies	retro_mmul_558, retro_mmul_88,
Monodelphis domestica	ENSMODG00000006575	1 retrocopy	retro_mdom_319,
Mustela putorius furo	ENSMPUG00000015253	1 retrocopy	retro_mputfur_1449,
Nomascus leucogenys	ENSNLEG00000002485	3 retrocopies	retro_nleu_1721, retro_nleu_3065, retro_nleu_837,
Ornithorhynchus anatinus	ENSOANG00000021532	1 retrocopy	retro_oana_33,
Otolemur garnettii	ENSOGAG00000001465	3 retrocopies	retro_ogar_2308, retro_ogar_2951, retro_ogar_552,
Pongo abelii	ENSPPYG00000018776	3 retrocopies	retro_pabe_1253, retro_pabe_2504, retro_pabe_387,
Pan troglodytes	ENSPTRG00000020457	3 retrocopies	retro_ptro_1019, retro_ptro_2040, retro_ptro_234,
Sus scrofa	ENSSSCG00000006079	1 retrocopy	retro_sscr_834 ,
Ictidomys tridecemlineatus	ENSSTOG00000011452	4 retrocopies	retro_itri_1591, retro_itri_192, retro_itri_605, retro_itri_894,
Tarsius syrichta	ENSTSYG00000003085	6 retrocopies	retro_tsyr_120, retro_tsyr_1541, retro_tsyr_226, retro_tsyr_373, retro_tsyr_624, retro_tsyr_798,
Tursiops truncatus	ENSTTRG00000016066	5 retrocopies	retro_ttru_1282, retro_ttru_1589, retro_ttru_1626, retro_ttru_369, retro_ttru_909,
Vicugna pacos	ENSVPAG00000008277	3 retrocopies	retro_vpac_30, retro_vpac_358, retro_vpac_89,