RetrogeneDB ID: retro_sscr_980

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:114287401..114288517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000009117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSSSCG00000006193
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_sscr_980
ATGACGTTTCGTAAGAAGGGCACCAAGAACCCCCCGGTCCTGAGCCAGGAATTCCTTCTGCAGAATCATGCGGACCTTGT
CGCCTGTGTGGGGATGTTCTTCGTGCTGGGGCTCATGTTCGAGGGAACAGCAGAAGTGTCTATCGTTTTTATTACTCTCC
AGCACGGCGTTACCTTCCCTGCAGCAGAAGCAGAACGAGCCACAGGATCCAAGTTGCTTTATTATTATGGTATCAAAGAT
TTGGCCACGGTGTTCTTCTACATGCTGGTGGCAATCATCATTCATGCCACCATTCAGGAGTATGTGTTGGATAGAATTAA
CAGGCGAATGCAACTCCCCAAACCAAAACAAAGCAAATTTAATGAATCGGGTCAGTTCAGTGTATTCTTTCTTGTCTCCT
CTATTTGGGGCACATTCATTCTAGTCTCTGAAAACTGCCTGGCAGACCTCTCTCTGTTATGGAGGGCTCATACCCATAAC
ATGATGACATTTCAGATGAAGTTCTTCTACATCTCACAATTGGCTTACTGGTTTCACGCCTTTCCTGAACTCTACTTCCA
GAGAATCAGACAACAGGATCTCCCCCATCAAGTTGTCTACGTTGGTCTCCACCTTTTTCACATTGCTGGGGCTTATCTCT
TGTACTTGAATCACCTAGGACTTGTCCTTTTGATGATGCATTATTTTGTTGAATTCCTTTCTCATGTTTGCGACCTGTTT
AACTTTGGTGATGAAAAATACCAGAAAGAGTTTTCTCTGTGGGCCATTGTGTTTATTTTGGGTCGGCTTGCGACTTTAAT
TGTTTCTCTCATCACAGTTGGTTTCCACCTGGCTGAAGGACAGAATCAGAATCCTGATGCCACTACTGAAAACGTGAACG
TGTTGGCAGCAAAAATTGCTGTTTTGTCATCCAGTTGCACCATCCAAGCATACATAACATGGAATTTATTTAATGCCCAG
CTTCAGTGGTGGATGGAAGAAGACATTCCTCTTCAGGCCCCAAGTGTGAAGAAGAAGCAACGGACTAAATGCAAGTCTTC
TAGAAAAGGAACAGAAAATGGAGTGGCAACTTCAGATAGAGTAGACTCTCCCCATAAGAGGAAAGAAAAATCTTCA

Alignment

ORF - retro_sscr_980 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRKKSTKSPPVLSHEFVLQNHADIVSCMAMVFLLGLMFEITAKASIIFVTLQYNVTLPATE-EQATES
          M..RKK.TK.PPVLS.EF.LQNHAD.V.C..M.F.LGLMFE.TA..SI.F.TLQ..VT.PA.E.E.AT.S
Retrocopy MTFRKKGTKNPPVLSQEFLLQNHADLVACVGMFFVLGLMFEGTAEVSIVFITLQHGVTFPAAEAERATGS

Parental  AFLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFSCIWGTFI
          ..LYYYGIKDLATVFFYMLVAIIIHA.IQEYVLD.INRRM...K.K.SKFNESGQ.S.F.L.S.IWGTFI
Retrocopy KLLYYYGIKDLATVFFYMLVAIIIHATIQEYVLDRINRRMQLPKPKQSKFNESGQFSVFFLVSSIWGTFI

Parental  LISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAG
          L.SEN...D...LWRA..HN.MTFQMKFFYISQLAYWFHAFPELYFQ.....D.P.Q.VY.GL.LFHIAG
Retrocopy LVSENCLADLSLLWRAHTHNMMTFQMKFFYISQLAYWFHAFPELYFQRIRQQDLPHQVVYVGLHLFHIAG

Parental  AYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARA
          AYLL.LNHLGLVLL..HYFVEFL.H...LF.F.DEKYQK.FSLWA..F.LGRL.TLI.S..TVGF.LA..
Retrocopy AYLLYLNHLGLVLLMMHYFVEFLSHVCDLFNFGDEKYQKEFSLWAIVFILGRLATLIVSLITVGFHLAEG

Parental  ENQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHS-TFQAPTVKKKPIVTKGRSSRK
          .NQ..D..T.N.NVLA..IAVL.S.C..QA...W...N.QL..W.E.....QAP.VKKK...TK..SSRK
Retrocopy QNQNPDATTENVNVLAAKIAVLSSSCTIQAYITWNLFNAQLQWWMEEDIPLQAPSVKKKQ-RTKCKSSRK

Parental  GTENGVNGTVTSNGADSPRNRKEKSS
          GTENGV....TS...DSP..RKEKSS
Retrocopy GTENGV---ATSDRVDSPHKRKEKSS

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	30.40 RPM
SRP014902_testis	0.57 RPM	73.55 RPM
SRP018288_heart	0.24 RPM	61.29 RPM
SRP018288_kidney	0.00 RPM	99.39 RPM
SRP018288_liver	0.00 RPM	136.56 RPM
SRP018288_lung	0.10 RPM	251.82 RPM
SRP018856_adipose	0.00 RPM	43.93 RPM
SRP035408_brain	0.64 RPM	9.02 RPM
SRP035408_liver	0.00 RPM	121.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_980 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_980 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_24

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980 ,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,