RetrogeneDB ID: retro_sscr_986

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:146032378..146032629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006807
• Aliases: None
• Description: None

Sequence

>retro_sscr_986
ACCCTGGAGCAGCACCTCGAGGACACAGTGAAGACTCCACCCACTGTTGAAGTCCTGCGCACAGACTCACGAGGACTGGA
GCGGGGCTGCCTCGGGACCCCGTCAGAGGAACGTGCCGGGAGAGCAATTCCAGCTCAGCAAGCAGCCAGGCTAACCTCTG
CTCCCACAATATTCCTGTGGAGAGCCTCGAATCAGATAATGGGAACATCAGGATCCAGACACATGATGGCATCCCAGTGG
CGGCGCAGGAA

Alignment

ORF - retro_sscr_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.12 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT-DIPVVCLESDNG
          TLEQHLEDT.K.P..V.VL.TDS.GL..GC.GT.S.E.AG.....AQQAA.LTS.PT..IPV..LESDNG
Retrocopy TLEQHLEDTVKTPPTVEVLRTDSRGLERGCLGTPSEERAG-RAIPAQQAARLTSAPT<NIPVESLESDNG

Parental  NIMIQKHDGITVAVHK
          NI.IQ.HDGI.VA...
Retrocopy NIRIQTHDGIPVAAQE

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	13.94 RPM
SRP014902_testis	0.00 RPM	29.28 RPM
SRP018288_heart	0.00 RPM	9.25 RPM
SRP018288_kidney	0.00 RPM	17.04 RPM
SRP018288_liver	0.00 RPM	4.16 RPM
SRP018288_lung	0.00 RPM	10.39 RPM
SRP018856_adipose	0.00 RPM	39.52 RPM
SRP035408_brain	0.00 RPM	3.40 RPM
SRP035408_liver	0.00 RPM	2.05 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_986 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_986 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1505

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011504	2 retrocopies	retro_amel_118, retro_amel_974,
Bos taurus	ENSBTAG00000014970	3 retrocopies	retro_btau_1505, retro_btau_1755, retro_btau_71,
Choloepus hoffmanni	ENSCHOG00000013405	3 retrocopies	retro_chof_2428, retro_chof_76, retro_chof_910,
Callithrix jacchus	ENSCJAG00000003438	1 retrocopy	retro_cjac_2918,
Dipodomys ordii	ENSDORG00000005672	3 retrocopies	retro_dord_147, retro_dord_642, retro_dord_775,
Equus caballus	ENSECAG00000021821	1 retrocopy	retro_ecab_1026,
Felis catus	ENSFCAG00000023792	5 retrocopies	retro_fcat_1718, retro_fcat_1853, retro_fcat_1887, retro_fcat_413, retro_fcat_478,
Homo sapiens	ENSG00000134248	1 retrocopy	retro_hsap_162,
Gorilla gorilla	ENSGGOG00000016522	1 retrocopy	retro_ggor_247,
Loxodonta africana	ENSLAFG00000012907	5 retrocopies	retro_lafr_1057, retro_lafr_1061, retro_lafr_1062, retro_lafr_665, retro_lafr_950,
Microcebus murinus	ENSMICG00000005264	4 retrocopies	retro_mmur_1114, retro_mmur_152, retro_mmur_422, retro_mmur_454,
Myotis lucifugus	ENSMLUG00000007198	2 retrocopies	retro_mluc_512, retro_mluc_708,
Macaca mulatta	ENSMMUG00000015023	4 retrocopies	retro_mmul_164, retro_mmul_2452, retro_mmul_440, retro_mmul_499,
Mustela putorius furo	ENSMPUG00000003833	5 retrocopies	retro_mputfur_1013, retro_mputfur_1020, retro_mputfur_1187, retro_mputfur_1387, retro_mputfur_921,
Mus musculus	ENSMUSG00000087260	3 retrocopies	retro_mmus_1061, retro_mmus_1901, retro_mmus_3723,
Oryctolagus cuniculus	ENSOCUG00000002449	2 retrocopies	retro_ocun_1880, retro_ocun_356,
Otolemur garnettii	ENSOGAG00000033478	2 retrocopies	retro_ogar_1388, retro_ogar_3454,
Ochotona princeps	ENSOPRG00000004283	5 retrocopies	retro_opri_138, retro_opri_199, retro_opri_488, retro_opri_567, retro_opri_716,
Pan troglodytes	ENSPTRG00000001078	2 retrocopies	retro_ptro_155, retro_ptro_436,
Sus scrofa	ENSSSCG00000006807	1 retrocopy	retro_sscr_986 ,
Ictidomys tridecemlineatus	ENSSTOG00000003401	5 retrocopies	retro_itri_1196, retro_itri_154, retro_itri_198, retro_itri_587, retro_itri_86,
Tupaia belangeri	ENSTBEG00000009117	5 retrocopies	retro_tbel_1220, retro_tbel_1427, retro_tbel_1756, retro_tbel_2289, retro_tbel_2329,
Tarsius syrichta	ENSTSYG00000006011	5 retrocopies	retro_tsyr_305, retro_tsyr_306, retro_tsyr_318, retro_tsyr_560, retro_tsyr_870,
Tursiops truncatus	ENSTTRG00000001319	1 retrocopy	retro_ttru_602,