RetrogeneDB ID: retro_sscr_351

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:168221319..168221532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM167A
• Ensembl ID: ENSSSCG00000029173
• Aliases: None
• Description: transmembrane protein 167A [Source:HGNC Symbol;Acc:28330]

Sequence

>retro_sscr_351
TCTGCCATTTTCAACTTTCAGAGTCTGTTGACTGTAATCTTGCTGCTTATATGTACCTCTACTTAAATCTGATCCTTGGC
ACCCAGCCTACTGGACAGAAATAAAACTGGATTGTTGGGTATACTTTGGAAGTGTGCTAGAATTGATGAACAGAAGAGTC
CTTATGTTGCAGTATGCTGTGTTGTGATGGCCTTCAGCATCCTCTTCATACAG

Alignment

ORF - retro_sscr_351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAIFNFQSLLTVILLLICTCAYIRSLAPSLLDRNKTGLLGIFWKCARIGERKSPYVAVCCVVMAFSILFI
          SAIFNFQSLLTVILLLICT...I.SLAPSLLDRNKTGLLGI.WKCARI.E.KSPYVAVCCVVMAFSILFI
Retrocopy SAIFNFQSLLTVILLLICTST*I*SLAPSLLDRNKTGLLGILWKCARIDEQKSPYVAVCCVVMAFSILFI

Parental  Q
          Q
Retrocopy Q

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	0.40 RPM	3.45 RPM
SRP014902_testis	0.28 RPM	3.25 RPM
SRP018288_heart	0.03 RPM	6.84 RPM
SRP018288_kidney	0.00 RPM	11.92 RPM
SRP018288_liver	0.00 RPM	12.63 RPM
SRP018288_lung	0.00 RPM	3.36 RPM
SRP018856_adipose	0.00 RPM	7.35 RPM
SRP035408_brain	0.00 RPM	4.86 RPM
SRP035408_liver	0.00 RPM	9.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_351 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_351 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_351 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039591	3 retrocopies	retro_btau_497, retro_btau_500, retro_btau_852,
Canis familiaris	ENSCAFG00000029436	1 retrocopy	retro_cfam_904,
Choloepus hoffmanni	ENSCHOG00000012009	14 retrocopies	retro_chof_1306, retro_chof_1548, retro_chof_1558, retro_chof_1681, retro_chof_1778, retro_chof_196, retro_chof_2109, retro_chof_2288, retro_chof_2444, retro_chof_2476, retro_chof_2663, retro_chof_2708, retro_chof_333, retro_chof_622,
Callithrix jacchus	ENSCJAG00000011238	3 retrocopies	retro_cjac_2328, retro_cjac_318, retro_cjac_929,
Cavia porcellus	ENSCPOG00000026186	2 retrocopies	retro_cpor_1123, retro_cpor_310,
Dasypus novemcinctus	ENSDNOG00000003073	21 retrocopies	retro_dnov_1345, retro_dnov_1443, retro_dnov_1521, retro_dnov_1612, retro_dnov_1633, retro_dnov_1648, retro_dnov_1756, retro_dnov_1852, retro_dnov_1888, retro_dnov_202, retro_dnov_2118, retro_dnov_2347, retro_dnov_2628, retro_dnov_319, retro_dnov_356, retro_dnov_448, retro_dnov_550, retro_dnov_806, retro_dnov_924, retro_dnov_948, retro_dnov_979,
Dipodomys ordii	ENSDORG00000015882	2 retrocopies	retro_dord_425, retro_dord_665,
Equus caballus	ENSECAG00000026834	2 retrocopies	retro_ecab_690, retro_ecab_995,
Erinaceus europaeus	ENSEEUG00000001023	2 retrocopies	retro_eeur_295, retro_eeur_457,
Echinops telfairi	ENSETEG00000016490	11 retrocopies	retro_etel_1079, retro_etel_1325, retro_etel_1617, retro_etel_1788, retro_etel_1817, retro_etel_1849, retro_etel_2072, retro_etel_276, retro_etel_706, retro_etel_897, retro_etel_959,
Felis catus	ENSFCAG00000012375	4 retrocopies	retro_fcat_1548, retro_fcat_180, retro_fcat_1986, retro_fcat_512,
Homo sapiens	ENSG00000174695	2 retrocopies	retro_hsap_1969, retro_hsap_4937,
Gorilla gorilla	ENSGGOG00000024191	1 retrocopy	retro_ggor_185,
Loxodonta africana	ENSLAFG00000009206	1 retrocopy	retro_lafr_1075,
Myotis lucifugus	ENSMLUG00000008924	3 retrocopies	retro_mluc_1281, retro_mluc_846, retro_mluc_884,
Monodelphis domestica	ENSMODG00000025616	3 retrocopies	retro_mdom_1169, retro_mdom_136, retro_mdom_862,
Mus musculus	ENSMUSG00000012422	9 retrocopies	retro_mmus_1220, retro_mmus_1988, retro_mmus_2520, retro_mmus_2898, retro_mmus_2899, retro_mmus_295, retro_mmus_2999, retro_mmus_381, retro_mmus_944,
Oryctolagus cuniculus	ENSOCUG00000009326	2 retrocopies	retro_ocun_1788, retro_ocun_659,
Otolemur garnettii	ENSOGAG00000009040	4 retrocopies	retro_ogar_1134, retro_ogar_1817, retro_ogar_2709, retro_ogar_2752,
Ochotona princeps	ENSOPRG00000004516	2 retrocopies	retro_opri_1158, retro_opri_231,
Pan troglodytes	ENSPTRG00000017053	1 retrocopy	retro_ptro_13,
Rattus norvegicus	ENSRNOG00000016686	3 retrocopies	retro_rnor_1754, retro_rnor_2049, retro_rnor_933,
Sorex araneus	ENSSARG00000005120	3 retrocopies	retro_sara_379, retro_sara_478, retro_sara_515,
Sarcophilus harrisii	ENSSHAG00000011984	4 retrocopies	retro_shar_209, retro_shar_262, retro_shar_599, retro_shar_627,
Sus scrofa	ENSSSCG00000029173	2 retrocopies	retro_sscr_1077, retro_sscr_351 ,
Tupaia belangeri	ENSTBEG00000002432	3 retrocopies	retro_tbel_1430, retro_tbel_2962, retro_tbel_4129,
Tarsius syrichta	ENSTSYG00000010018	1 retrocopy	retro_tsyr_1844,
Tursiops truncatus	ENSTTRG00000009033	2 retrocopies	retro_ttru_1375, retro_ttru_750,