RetrogeneDB ID: retro_sscr_640

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:123312740..123313505(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTBD10
• Ensembl ID: ENSSSCG00000013395
• Aliases: None
• Description: BTB (POZ) domain containing 10 [Source:HGNC Symbol;Acc:21445]

Sequence

>retro_sscr_640
TATAAACATTCAAGTGCTCCCTCACATGCTGCTAAAGGAGTCATTGACCACACCAAAATGAGTCTGCATGGTGCTAGTGA
GGAACATGAGAGATCAAGAGATAGACAAAGGTCAAGTGACAGATCACGAGACTCATCTCATGAAAGAACAGAATCCCAGC
TCACTCCTTGTCTTAGAAATGTTACTTCTCCAACACTGCAGCATCATACTGAATGTGAAAACGATCACAATTCCTCTTGT
CCAAGCAGTCCCTCGTCCTCAAAAAGCATCTCCAAATGGTTCCAGTAGCAGTGCTGGGAACAGCAGCAGAAACAATAGTC
ACTGAAGTTCAGATGGCAACTGTAAGACATCTGGGGAAGTGGTGTTTGTGTATGAAAATGAAAAAGAAAGAGCTCAGAAT
GTTAGAACATCAGAGCGAGTGACGCTGATAGTGGATAACACCATATTTGTTGTGGACCATCCATTTTTACTGCACAACCA
AATACAGTATTGGGCAGGATGTTTGGGTCTGGCAGATAACATAACTTTACACATCCCATTGAGAAGGGGTAGTATGAAGT
GGCAGAGGGCACTGGTTCTACTGAGTTTCAAGCTATTCTGGATTACTATAAAACAGGAATAATCCATTGTCTTGATGGCA
TATCTCTCCCTGAACTAAGAGAAGCATGTGACTATCTTTGTATCTCTTTTGAATATAGTACTATAAAATGTAGAGATCTC
AGTGCCCTCCTGCATGAGTTATCAAGTGATGGTGTTTGTAGACAG

Alignment

ORF - retro_sscr_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 52.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTKVSTPSRVAKGVVEHTKMSLHGASGGHERSRDRRRSSDRSRDSSHERTESQLTPCIRNVTSPTRQHHI
          Y...S.PS..AKGV..HTKMSLHGAS..HERSRDR.RSSDRSRDSSHERTESQLTPC.RNVTSPT.QHH.
Retrocopy YKHSSAPSHAAKGVIDHTKMSLHGASEEHERSRDRQRSSDRSRDSSHERTESQLTPCLRNVTSPTLQHHT

Parental  EREKDHSSSRPSSP-RPQKASPNGSSSSAGNSSRNSSQSSSDGNCKTSGEMVFVYENAKEGARNVRTSER
          E.E.DH.SS.PSSP.RPQKASPNGSSSSAGNSSRN.S..SSDGNCKTSGE.VFVYEN.KE.A.NVRTSER
Retrocopy ECENDHNSSCPSSP>RPQKASPNGSSSSAGNSSRNNSH*SSDGNCKTSGEVVFVYENEKERAQNVRTSER

Parental  VTLIVDNTRFVVD-PSIFTAQPNTMLGRMFGSGREHNFTRPNEKGEYEVAEGIGSTVFRAILDYYKTGII
          VTLIVDNT.FVVD.PSIFTAQPNT.LGRMFGSGR.HNFT.P.EKG.YEVAEG.GST.F.AILDYYKTGII
Retrocopy VTLIVDNTIFVVD<PSIFTAQPNTVLGRMFGSGR*HNFTHPIEKG*YEVAEGTGSTEFQAILDYYKTGII

Parental  RCPDGISIPELREACDYLCISFEYSTIKCRDLSALMHELSNDGARRQ
          .C.DGIS.PELREACDYLCISFEYSTIKCRDLSAL.HELS.DG..RQ
Retrocopy HCLDGISLPELREACDYLCISFEYSTIKCRDLSALLHELSSDGVCRQ

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	9.03 RPM
SRP014902_testis	0.00 RPM	17.82 RPM
SRP018288_heart	0.00 RPM	17.65 RPM
SRP018288_kidney	0.00 RPM	9.46 RPM
SRP018288_liver	0.00 RPM	2.88 RPM
SRP018288_lung	0.00 RPM	22.20 RPM
SRP018856_adipose	0.00 RPM	19.05 RPM
SRP035408_brain	0.00 RPM	66.92 RPM
SRP035408_liver	0.00 RPM	5.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_640 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_640 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024984	1 retrocopy	retro_cpor_137,
Monodelphis domestica	ENSMODG00000008728	1 retrocopy	retro_mdom_1020,
Mus musculus	ENSMUSG00000038187	1 retrocopy	retro_mmus_3560,
Nomascus leucogenys	ENSNLEG00000017691	1 retrocopy	retro_nleu_232,
Otolemur garnettii	ENSOGAG00000000739	1 retrocopy	retro_ogar_3201,
Pan troglodytes	ENSPTRG00000003377	1 retrocopy	retro_ptro_753,
Rattus norvegicus	ENSRNOG00000014341	2 retrocopies	retro_rnor_2220, retro_rnor_2872,
Sorex araneus	ENSSARG00000000266	1 retrocopy	retro_sara_405,
Sus scrofa	ENSSSCG00000013395	2 retrocopies	retro_sscr_639, retro_sscr_640 ,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tursiops truncatus	ENSTTRG00000013943	1 retrocopy	retro_ttru_897,