RetrogeneDB ID: retro_sscr_10

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:161087946..161088600(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000011944
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSSSCG00000006821
• Aliases: None
• Description: glutathione S-transferase mu 3 (brain) [Source:HGNC Symbol;Acc:4635]

Sequence

>retro_sscr_10
GCCATTACCCTGGGTTACTGGGACATCCGCGGGCTGGCTCACGCCATCCGCCTGCTCCTGGAATACACAGGTTCAAATTA
TGAGGAGAGGAAATACATGATGGGAGATCCTCCTGACTATGACAGAAGCCAGTGGTTGAATGAAAGATCCAAGCTGGGCC
TGGACTTCCCCAATTTGCCCTACTTAATTGATGGGCCTCACAAGCTCACCCAGAGCAATGCCATCCTTCGCTACATTGCT
CGCAAGCACAACATGTGTGGGGAGACAGAGAAGGAGAAGATTCAAGTGGACATTCTGGAGAGCCAGGTTATGGATGTACG
CTTACACATGGCCAGGGTCTGCTACAGCTCTGACTTTGAGAAACTGAAGCCTGGTTATGTGGACGAGATCCCTGAGAAGA
TGAGGCTCTTCTCAGCGTTTTTGGGGAAGGGGCCTTGGTTTGCAGGACACACGCTCACCTATGTAGATTTCCTGGCTTAC
GACATCCTTGATCTACATCGCATATTTGAGCCCAAGTGCCTGGATGAATTCCCAAACCTGAAAGACTTCATCACCCGCTT
TGAGGGGCTTAAGAAGATCTCTGCTTACATGAAGTCTAGTCGCTTCCTCCCACGCCCTTTGTTTCTAAAGATTGCCATGT
GGGGTAACAAGTAG

Alignment

ORF - retro_sscr_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.28 %
• Parental protein coverage: 94.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SMVLGYWDIRGLAHAIRMLLEFTDTSYEEKRYICGEAPDYDRSQWLDVKYKLDLDFPNLPYLMDGKNKLT
          ...LGYWDIRGLAHAIR.LLE.T...YEE..Y..G..PDYDRSQWL....KL.LDFPNLPYL.DG..KLT
Retrocopy AITLGYWDIRGLAHAIRLLLEYTGSNYEERKYMMGDPPDYDRSQWLNERSKLGLDFPNLPYLIDGPHKLT

Parental  QSNAILRYIARKHNMCGETEEEKIRVDIMENQIMDFRMQLIRLCYSPDHEKLKPQYLEQLPGQLKQFSLF
          QSNAILRYIARKHNMCGETE.EKI.VDI.E.Q.MD.R....R.CYS.D.EKLKP.Y....P.....FS.F
Retrocopy QSNAILRYIARKHNMCGETEKEKIQVDILESQVMDVRLHMARVCYSSDFEKLKPGYVDEIPEKMRLFSAF

Parental  LGKYSWFAGEKLTFVDFLTYDVLDQNRIFEPRCLDEFPNLKAFMCRFEALEKIAAYMQSDRFLKMPINNK
          LGK..WFAG..LT.VDFL.YD.LD..RIFEP.CLDEFPNLK.F..RFE.L.KI.AYM.S.RFL..P...K
Retrocopy LGKGPWFAGHTLTYVDFLAYDILDLHRIFEPKCLDEFPNLKDFITRFEGLKKISAYMKSSRFLPRPLFLK

Parental  MAQWGNK
          .A.WGNK
Retrocopy IAMWGNK

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	1.86 RPM	3.19 RPM
SRP014902_testis	1.41 RPM	22.07 RPM
SRP018288_heart	0.03 RPM	0.05 RPM
SRP018288_kidney	0.00 RPM	0.69 RPM
SRP018288_liver	0.48 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	1.32 RPM
SRP018856_adipose	4.16 RPM	4.79 RPM
SRP035408_brain	0.79 RPM	12.13 RPM
SRP035408_liver	14.12 RPM	3.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_10 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_10 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10 , retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,