RetrogeneDB ID: retro_sscr_1178

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:131523300..131523740(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IMMP1L
• Ensembl ID: ENSSSCG00000013322
• Aliases: None
• Description: IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) [Source:HGNC Symbol;Acc:26317]

Sequence

>retro_sscr_1178
ATGCTTCGTGGTATTCTGGGAAAAACCTTTCAACTTGTTGGCTATACTATTCAGTGTGGCTGTATAGCTCATTGTGCTTT
TGAATGTGTTGGTGGTGTTATGCGTTCTGGACCATCAATGGAGCCTACAATTCAAAATTCAGATATTGTCTTTGCAGAAA
ATCCTAGTTGACATTTTTGTAGTATCCAGAGAGGTGATATTGTGATTGCAAAAGCCTGAGTGATCCAAAATCAAATATTT
ATAAAAGAGTAGTTGGTTTGGAGGAAGACAAAATTCTCACCAATAGTCAATCAGATTTCTTTAAAGGTCATAGTTATGTG
CCAACAGGTCACATTTAGTTAGAAGGTGATAATCTACAGAATTCTACACATTCCAGGTACTATGGACTTGTTCCATATGG
ACTGATAGGAAGATATATCTTCTTTAAGATTTGGCCTCTG

Alignment

ORF - retro_sscr_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.89 %
• Parental protein coverage: 89.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRGVLGKTFRLVGYTIQYGCIAHCAFEYVGGVVMCSGPSMEPTIQNPDIVFAENLSRHFYSIQRGDIVI
          MLRG.LGKTF.LVGYTIQ.GCIAHCAFE.VGGV.M.SGPSMEPTIQN.DIVFAEN.S.HF.SIQRGDIVI
Retrocopy MLRGILGKTFQLVGYTIQCGCIAHCAFECVGGV-MRSGPSMEPTIQNSDIVFAENPS*HFCSIQRGDIVI

Parental  AK-SPSDPKSNICKRVIGLEGDKILTNSPSGFFKGHSYVPTGHVWLEGDNLQNSTDSRYYGPVPYGLIRG
          AK.S.SDPKSNI.KRV.GLE.DKILTNS.S.FFKGHSYVPTGH..LEGDNLQNST.SRYYG.VPYGLI..
Retrocopy AK<SLSDPKSNIYKRVVGLEEDKILTNSQSDFFKGHSYVPTGHI*LEGDNLQNSTHSRYYGLVPYGLIGR

Parental  RIFFKIWPL
          .IFFKIWPL
Retrocopy YIFFKIWPL

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	1.73 RPM
SRP014902_testis	0.00 RPM	4.53 RPM
SRP018288_heart	0.00 RPM	15.35 RPM
SRP018288_kidney	0.00 RPM	11.03 RPM
SRP018288_liver	0.00 RPM	7.04 RPM
SRP018288_lung	0.00 RPM	1.73 RPM
SRP018856_adipose	0.00 RPM	3.39 RPM
SRP035408_brain	0.00 RPM	1.46 RPM
SRP035408_liver	0.00 RPM	3.32 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1178 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006876	1 retrocopy	retro_amel_623,
Bos taurus	ENSBTAG00000000475	1 retrocopy	retro_btau_528,
Canis familiaris	ENSCAFG00000007514	2 retrocopies	retro_cfam_1757, retro_cfam_548,
Choloepus hoffmanni	ENSCHOG00000010106	4 retrocopies	retro_chof_1157, retro_chof_1665, retro_chof_2427, retro_chof_358,
Callithrix jacchus	ENSCJAG00000006042	1 retrocopy	retro_cjac_1240,
Dipodomys ordii	ENSDORG00000000250	4 retrocopies	retro_dord_144, retro_dord_205, retro_dord_243, retro_dord_726,
Equus caballus	ENSECAG00000020512	3 retrocopies	retro_ecab_1019, retro_ecab_159, retro_ecab_920,
Echinops telfairi	ENSETEG00000003057	1 retrocopy	retro_etel_1971,
Homo sapiens	ENSG00000148950	1 retrocopy	retro_hsap_786,
Gorilla gorilla	ENSGGOG00000014897	1 retrocopy	retro_ggor_651,
Myotis lucifugus	ENSMLUG00000006504	2 retrocopies	retro_mluc_2105, retro_mluc_385,
Macaca mulatta	ENSMMUG00000016806	1 retrocopy	retro_mmul_1092,
Mus musculus	ENSMUSG00000042670	2 retrocopies	retro_mmus_2571, retro_mmus_591,
Nomascus leucogenys	ENSNLEG00000017882	1 retrocopy	retro_nleu_2484,
Oryctolagus cuniculus	ENSOCUG00000029612	1 retrocopy	retro_ocun_388,
Otolemur garnettii	ENSOGAG00000007853	3 retrocopies	retro_ogar_1202, retro_ogar_2006, retro_ogar_2643,
Pongo abelii	ENSPPYG00000003389	1 retrocopy	retro_pabe_747,
Pan troglodytes	ENSPTRG00000003472	1 retrocopy	retro_ptro_547,
Pteropus vampyrus	ENSPVAG00000015535	1 retrocopy	retro_pvam_932,
Rattus norvegicus	ENSRNOG00000004829	1 retrocopy	retro_rnor_2450,
Sarcophilus harrisii	ENSSHAG00000015407	2 retrocopies	retro_shar_396, retro_shar_491,
Sus scrofa	ENSSSCG00000013322	1 retrocopy	retro_sscr_1178 ,
Ictidomys tridecemlineatus	ENSSTOG00000003179	2 retrocopies	retro_itri_489, retro_itri_623,
Tupaia belangeri	ENSTBEG00000002126	6 retrocopies	retro_tbel_1510, retro_tbel_2503, retro_tbel_315, retro_tbel_3504, retro_tbel_4049, retro_tbel_878,
Tarsius syrichta	ENSTSYG00000009257	1 retrocopy	retro_tsyr_2139,
Tursiops truncatus	ENSTTRG00000002395	2 retrocopies	retro_ttru_1862, retro_ttru_966,
Vicugna pacos	ENSVPAG00000001940	1 retrocopy	retro_vpac_126,