RetrogeneDB ID: retro_sscr_167

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:105953385..105953629(-)
• Located in intron of: ENSSSCG00000004499

Retrocopy information

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

Parental gene information

• Parental gene symbol: DBI
• Ensembl ID: ENSSSCG00000023435
• Aliases: None
• Description: Sus scrofa diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein) (DBI), mRNA. [Source:RefSeq mRNA;Acc:NM_214119]

Sequence

>retro_sscr_167
ATGTCTCAGGTAGAGTCTGAGAAAAGCTGCTGAGGAAGTTAAGAACCTCAAGACCAAGCCAGCAGATGAGATGCTGTTCA
TCTAAGGCTACTACAAACAAGCAACCGGAGGTGACATAAGTATAGAACGACCTGGTATGTTGGAGCTCAAAGGCAAGGCC
AAATGGGATGAGCTGAAACAGACTTCGAAGGAAGATGCCATGACAGTGTAAGTCAACAAAGTAGAAGTAAAGAAAATACA
TGGA

Alignment

ORF - retro_sscr_167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 98.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQAEFEK-AAEEVKNLKTKPADDEMLFIYSHYKQATVGDINTERPGILDLKGKAKWDAWNGLKGTSKED
          MSQ.E.EK.AAEEVKNLKTKPAD.EMLFI...YKQAT.GDI..ERPG.L.LKGKAKWD....LK.TSKED
Retrocopy MSQVESEK>AAEEVKNLKTKPAD-EMLFI*GYYKQATGGDISIERPGMLELKGKAKWDE---LKQTSKED

Parental  AMKAYINKVEELKKKYG
          AM....NKV.E.KK..G
Retrocopy AMTV*VNKV-EVKKIHG

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	0.66 RPM	10.22 RPM
SRP014902_testis	0.99 RPM	29.28 RPM
SRP018288_heart	2.04 RPM	54.88 RPM
SRP018288_kidney	1.28 RPM	147.56 RPM
SRP018288_liver	1.60 RPM	177.50 RPM
SRP018288_lung	0.41 RPM	41.95 RPM
SRP018856_adipose	1.04 RPM	552.16 RPM
SRP035408_brain	0.13 RPM	379.82 RPM
SRP035408_liver	0.23 RPM	680.73 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_167 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_167 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008509	3 retrocopies	retro_amel_1587, retro_amel_69, retro_amel_993,
Bos taurus	ENSBTAG00000009517	2 retrocopies	retro_btau_154, retro_btau_1718,
Canis familiaris	ENSCAFG00000004895	6 retrocopies	retro_cfam_1228, retro_cfam_134, retro_cfam_1452, retro_cfam_1599, retro_cfam_570, retro_cfam_857,
Callithrix jacchus	ENSCJAG00000021436	1 retrocopy	retro_cjac_954,
Cavia porcellus	ENSCPOG00000000415	2 retrocopies	retro_cpor_576, retro_cpor_59,
Equus caballus	ENSECAG00000018949	1 retrocopy	retro_ecab_14,
Erinaceus europaeus	ENSEEUG00000012115	2 retrocopies	retro_eeur_101, retro_eeur_33,
Echinops telfairi	ENSETEG00000000220	5 retrocopies	retro_etel_1131, retro_etel_1403, retro_etel_1761, retro_etel_754, retro_etel_849,
Homo sapiens	ENSG00000155368	3 retrocopies	retro_hsap_1619, retro_hsap_3345, retro_hsap_3617,
Gorilla gorilla	ENSGGOG00000010372	3 retrocopies	retro_ggor_1224, retro_ggor_1289, retro_ggor_2442,
Loxodonta africana	ENSLAFG00000005002	2 retrocopies	retro_lafr_280, retro_lafr_42,
Microcebus murinus	ENSMICG00000000294	2 retrocopies	retro_mmur_1233, retro_mmur_291,
Macaca mulatta	ENSMMUG00000011126	3 retrocopies	retro_mmul_168, retro_mmul_651, retro_mmul_757,
Monodelphis domestica	ENSMODG00000000393	1 retrocopy	retro_mdom_61,
Mustela putorius furo	ENSMPUG00000000945	2 retrocopies	retro_mputfur_170, retro_mputfur_438,
Mus musculus	ENSMUSG00000026385	2 retrocopies	retro_mmus_2307, retro_mmus_712,
Nomascus leucogenys	ENSNLEG00000010290	2 retrocopies	retro_nleu_1170, retro_nleu_807,
Oryctolagus cuniculus	ENSOCUG00000004566	1 retrocopy	retro_ocun_234,
Ochotona princeps	ENSOPRG00000008363	3 retrocopies	retro_opri_125, retro_opri_594, retro_opri_794,
Pongo abelii	ENSPPYG00000012788	2 retrocopies	retro_pabe_2755, retro_pabe_2968,
Pan troglodytes	ENSPTRG00000012401	2 retrocopies	retro_ptro_2140, retro_ptro_2446,
Pteropus vampyrus	ENSPVAG00000014349	5 retrocopies	retro_pvam_1120, retro_pvam_1121, retro_pvam_168, retro_pvam_529, retro_pvam_85,
Rattus norvegicus	ENSRNOG00000046889	3 retrocopies	retro_rnor_1801, retro_rnor_2737, retro_rnor_879,
Sus scrofa	ENSSSCG00000023435	3 retrocopies	retro_sscr_167 , retro_sscr_375, retro_sscr_41,
Ictidomys tridecemlineatus	ENSSTOG00000006759	1 retrocopy	retro_itri_1,
Tupaia belangeri	ENSTBEG00000002067	13 retrocopies	retro_tbel_1617, retro_tbel_2338, retro_tbel_2726, retro_tbel_273, retro_tbel_3096, retro_tbel_3097, retro_tbel_3305, retro_tbel_3392, retro_tbel_3454, retro_tbel_3602, retro_tbel_4015, retro_tbel_556, retro_tbel_579,
Tarsius syrichta	ENSTSYG00000002108	2 retrocopies	retro_tsyr_142, retro_tsyr_1654,