RetrogeneDB ID: retro_sscr_537

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:10069196..10069728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSSSCG00000026283
• Aliases: None
• Description: UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]

Sequence

>retro_sscr_537
ATTTGTGAAACAGAATCTGACAACCACACTCTTAGCGGTAGTTGAAAAATGAACTATGACTATTTTATTAACAGCCTTTG
AAGAGGAATAGCTCAGAAGACTGATGCTCACTTCTTGTCGCCCACTAAAAAAGAGGAATAGGTGAATGTCAGCATACAAA
ACTTGAAAAATTGATTCTAAGTCACTAATGATTTCAGAAGTTATTCTGATGATGCAAGACACTAGGTTCTGAACATCATT
AAAATGGTGAATTAGCTTTAGAATTACAAGGGATTTTTGATAAAGCAGTTAGTGTTAAAATCAAAGATTTAAAAAATGAA
GTATGTATGTAGATGAAGCTGGTATTCTAGACCTTCCCAGCACATGGTCACAGACTAGAAAGTGCCACACCAAATTTTTT
TCTAAAGAGAACAATATCGATGATGAGAATAAAGATCACCCACCTGTTTCTTCACTAAAGAATCTGGATCATTTCACTAA
AATACAGATCTGTTTAGCCAAATGAAAAAGGATCATCCAGAAATTGTATATT

Alignment

ORF - retro_sscr_537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.38 %
• Parental protein coverage: 69.26 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VCETGSDHQPLSDNQQINCEYFVDSLFEE-AQKVGAKSLSPTEQKKQVDVSIKLWKNGFTVNDDFRSYSD
          .CET.SD...LS.....N..YF..SL....AQK..A..LSPT.....V.VSI...KN.F.V..DFRSYSD
Retrocopy ICETESDNHTLSGS*KMNYDYFINSL*RGIAQKTDAHFLSPTKKEE*VNVSIQNLKN*F*VTNDFRSYSD

Parental  GASQQFLNSIK-KGELPLELQGVFDKEEVDVRVEDKKNEVCMSTKPVFQPFSGQGHRLGSATP-KIVSKA
          .A....LN.IK..GEL.LELQG.FDK..V.V...D.KNEVCM..K.VF..F...GHRL.SATP.K..SK.
Retrocopy DARH*VLNIIK<NGELALELQGIFDK-AVSVKIKDLKNEVCM*MKLVF*TFPAHGHRLESATP<KFFSKE

Parental  KSIEVENKNKLSTVPLNNLEPITNVQIWLANGKRIVQKFNI
          ..I..ENK.......L.NL...T..QI.LA..KRI.QK..I
Retrocopy NNIDDENKDHPPVSSLKNLDHFTKIQICLAK*KRIIQKLYI

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	0.80 RPM
SRP014902_testis	0.00 RPM	2.97 RPM
SRP018288_heart	0.00 RPM	8.36 RPM
SRP018288_kidney	0.00 RPM	4.93 RPM
SRP018288_liver	0.00 RPM	1.76 RPM
SRP018288_lung	0.00 RPM	6.82 RPM
SRP018856_adipose	0.00 RPM	2.52 RPM
SRP035408_brain	0.00 RPM	2.70 RPM
SRP035408_liver	0.00 RPM	2.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_537 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_537 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_537 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537 ,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,