RetrogeneDB ID: retro_sscr_616

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:53704336..53705101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000002036
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:F1S9C9]

Sequence

>retro_sscr_616
CTGGCCAGCATGTTAGAGATGCCACTCGCCATGAACCAGGACCAGTTTTACAGACAAGGGGATCATGTGGATCTGCCGGA
CCTTGGTCCAGGGTACCCTGGCAATGGACTGAGCCTGGTAGTGCCCAGTGGGGGTGTCCCAGAGGAGCCGAGAATCAAAA
TGCTTCACCATACCACCATCCTGGCCTTCAAGATTCTCCTTGGAGTCATTGTTGCAGCAGACTCCTGGGACATGGCAGTT
GCCTACATTGCCTCCCAGACAGTCAAAAATGTGATAGAGATCAGCCTGTACCTGCTGGCCACTGGGGCTGTAGGTGCAGT
GAATTGCAGGTTCCTGGCTCAGCAGTGATGAATCTATGAGCTTCAAAACAAGGGATGCATCTCAGTAGCAGCTGCCTCCA
AGCTGCTTGCCAACATGGTGTATCAGTATAAAGGCATGGGGCTGTCCATGGGCACCATGATCTGTGTTTGGGGTAAGAGA
GGCCCTGGCCTCTACTATATGGACAGTGAAGGAAACTGGATCTGGGGGGTGGACTTCTCTGTAGGTTCTAGATCTGTGCA
TGCTTATGGGTTCATGGGTTACTCCTATGACCTGGAGGTGGAACGGGCTTATGATATGGCCAGTCAAGCCACCTATTAAG
CCAGCTAAAGTGATGCCTACTCAGGAGGCTTGGTCAACCTCTACCATGTCTGGGAGGATGGCTGGATCCAAAGCTCCAGT
GACAATGTAGCTTATCTACATTACAAGTATAGTGAATTTTCACCC

Alignment

ORF - retro_sscr_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.65 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LASVLERPLAVNRRGFFGFGGRADLLDLGPGSPGDGLSLVAPSWGVPEEPRIEMLHGTTTLAFKFLHGVI
          LAS.LE.PLA.N...F...G...DL.DLGPG.PG.GLSLV.PS.GVPEEPRI.MLH.TT.LAFK.L.GVI
Retrocopy LASMLEMPLAMNQDQFYRQGDHVDLPDLGPGYPGNGLSLVVPSGGVPEEPRIKMLHHTTILAFKILLGVI

Parental  VAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLL
          VAADS...A.AYIASQTVK.VIEI..YLL.T.A.GA..C....R.LA.Q..IYEL.NK..ISVAAASKLL
Retrocopy VAADSWDMAVAYIASQTVKNVIEISLYLLATGAVGAVNC----RFLAQQ**IYELQNKGCISVAAASKLL

Parental  ANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAY
          ANMVYQYKGMGLSMGTMIC.W.KRGPGLYY.DSEGN.I.G..FSVGS.SV.AYG.M..GYSYDLEVE.AY
Retrocopy ANMVYQYKGMGLSMGTMICVWGKRGPGLYYMDSEGNWIWGVDFSVGSRSVHAYGFM--GYSYDLEVERAY

Parental  DLARRAIYQATYRDAYSGGSVNLYHVREDGWIRVSSDNVADLHDKYSESTP
          D.A..A.Y.A...DAYSGG.VNLYHV.EDGWI..SSDNVA.LH.KYSE..P
Retrocopy DMASQATY*AS*SDAYSGGLVNLYHVWEDGWIQSSSDNVAYLHYKYSEFSP

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	74.73 RPM
SRP014902_testis	0.00 RPM	117.40 RPM
SRP018288_heart	0.00 RPM	50.32 RPM
SRP018288_kidney	0.00 RPM	83.04 RPM
SRP018288_liver	0.00 RPM	59.17 RPM
SRP018288_lung	0.00 RPM	38.29 RPM
SRP018856_adipose	0.31 RPM	114.06 RPM
SRP035408_brain	0.00 RPM	59.80 RPM
SRP035408_liver	0.00 RPM	59.94 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_616 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_616 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616 ,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90,