RetrogeneDB ID: retro_sscr_1

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:147721373..147722366(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000029716
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: WDR5
• Ensembl ID: ENSSSCG00000024912
• Aliases: None
• Description: WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]

Sequence

>retro_sscr_1
ATGGCTACAAAGGAGTCAAGAGATGACAAAGCCGGGTCCGCCCTCTCCTCATCAGCCAATCAGAGCAAGCAAGTCGCTGA
AAAACCAAACTACACGCTCAAATTTACTCTCGTGGGACATACGGAAGCAGTATCATCAGTGAAATTTAGTCCTAATGGAG
AATGGCTAGCAAGTTCTTCTGCTGATAAAGTAATTATAATTTGGGGAGCCTATGATGGAAAATATGAGAAAGCACTTAAA
GGACACAGTCTGGAAATATCAGATGTTGCCTGGTCATCAGATTCCGGGCGTCTTGTTTCTGCCTCAGATGATAAAACTCT
AAAGATTTGGGATGTGAGAGTTGGAAAATGTTTGAAAACGCTGAAAGGGCACAGTAATTATGTTTTTTGTTGTAATTTCA
ACCCACCATCCAACCTCATCATTTCAGGATCTTTTGATGAGAGCGTGAAAATATGGGAGGTGAAAACAGGAAGGTGCCTT
AAGACTTTGTCTGCTCATTCTGATCCAGTTTCTGCTGTTCATTTTAATTGTAAGGGGTCCTTGATAGTGTCAGGTAGCTA
TGATGGTGTCTGTCGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAAACACTGGTTGATGATGATAACCCTCCAATCT
CTTTTGTAAAATTTTCTCCAAATGGTAAATATATTCTCATTGCAACTTTGGACAATACTCTTAAACTGTGGGATTACAGC
AGAGGCAGATGCCTGAAGACATACACTGGTCATAAGAATGAGAAATACTGCATATTTGCCAATTTTTCAGTCACTAGTGG
AAAGTGGATTGTGTCTGGTTCAGAAGATAACCTGGTTTACATTTGGAACCTTCAGACTAAAGAGATTGTACAGAAATTAC
AAGGTCATACAGATGTTGTGATCTCAGCAGCTTGTCATCCTACAGAAAACATTATTGCATCAGCAGCATTAGGAAATGAC
AAAACAGTTAAACTGTGGATGAGTAACTACTAA

Alignment

ORF - retro_sscr_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATEEKKPETEAARAQPAPSAAATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIK
          MAT.E.........A..A.S..A.QSK....KPNY.LKFTL.GHT.AVSSVKFSPNGEWLASSSADK.I.
Retrocopy MATKESRDD----KAGSALSSSANQSKQVAEKPNYTLKFTLVGHTEAVSSVKFSPNGEWLASSSADKVII

Parental  IWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQ
          IWGAYDGK.EK...GH.L.ISDVAWSSDS..LVSASDDKTLKIWDV..GKCLKTLKGHSNYVFCCNFNP.
Retrocopy IWGAYDGKYEKALKGHSLEISDVAWSSDSGRLVSASDDKTLKIWDVRVGKCLKTLKGHSNYVFCCNFNPP

Parental  SNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLI
          SNLI.SGSFDESV.IW.VKTG.CLKTL.AHSDPVSAVHFN..GSLIVS.SYDG.CRIWD.ASGQCLKTL.
Retrocopy SNLIISGSFDESVKIWEVKTGRCLKTLSAHSDPVSAVHFNCKGSLIVSGSYDGVCRIWDAASGQCLKTLV

Parental  DDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSED
          DDDNPP.SFVKFSPNGKYIL.ATLDNTLKLWDYS.G.CLKTYTGHKNEKYCIFANFSVT.GKWIVSGSED
Retrocopy DDDNPPISFVKFSPNGKYILIATLDNTLKLWDYSRGRCLKTYTGHKNEKYCIFANFSVTSGKWIVSGSED

Parental  NLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSD
          NLVYIWNLQTKEIVQKLQGHTDVVIS.ACHPTENIIASAAL.NDKT.KLW.S.
Retrocopy NLVYIWNLQTKEIVQKLQGHTDVVISAACHPTENIIASAALGNDKTVKLWMSN

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	0.66 RPM	45.53 RPM
SRP014902_testis	2.83 RPM	56.44 RPM
SRP018288_heart	2.28 RPM	14.46 RPM
SRP018288_kidney	4.33 RPM	31.32 RPM
SRP018288_liver	2.88 RPM	25.91 RPM
SRP018288_lung	7.43 RPM	30.75 RPM
SRP018856_adipose	1.69 RPM	27.20 RPM
SRP035408_brain	1.27 RPM	41.10 RPM
SRP035408_liver	2.99 RPM	36.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_sscr_1 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EW634687	147721928	147722140	100	212	0	212

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_11
Pan troglodytes	retro_ptro_18
Gorilla gorilla	retro_ggor_171
Macaca mulatta	retro_mmul_190
Callithrix jacchus	retro_cjac_1
Mus musculus	retro_mmus_132
Rattus norvegicus	retro_rnor_258
Bos taurus	retro_btau_299
Canis familiaris	retro_cfam_128
Equus caballus	retro_ecab_82

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011179	1 retrocopy	retro_amel_29,
Bos taurus	ENSBTAG00000047031	1 retrocopy	retro_btau_299,
Canis familiaris	ENSCAFG00000019830	1 retrocopy	retro_cfam_128,
Callithrix jacchus	ENSCJAG00000010123	1 retrocopy	retro_cjac_1,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Dipodomys ordii	ENSDORG00000015010	1 retrocopy	retro_dord_7,
Equus caballus	ENSECAG00000017389	1 retrocopy	retro_ecab_82,
Echinops telfairi	ENSETEG00000015731	1 retrocopy	retro_etel_15,
Felis catus	ENSFCAG00000005712	1 retrocopy	retro_fcat_119,
Homo sapiens	ENSG00000196363	1 retrocopy	retro_hsap_11,
Gorilla gorilla	ENSGGOG00000004997	2 retrocopies	retro_ggor_171, retro_ggor_2023,
Loxodonta africana	ENSLAFG00000011192	1 retrocopy	retro_lafr_55,
Microcebus murinus	ENSMICG00000008085	1 retrocopy	retro_mmur_34,
Myotis lucifugus	ENSMLUG00000002236	1 retrocopy	retro_mluc_11,
Macaca mulatta	ENSMMUG00000014159	1 retrocopy	retro_mmul_190,
Mustela putorius furo	ENSMPUG00000012184	1 retrocopy	retro_mputfur_2,
Mus musculus	ENSMUSG00000026917	1 retrocopy	retro_mmus_132,
Nomascus leucogenys	ENSNLEG00000013472	1 retrocopy	retro_nleu_63,
Otolemur garnettii	ENSOGAG00000008960	1 retrocopy	retro_ogar_86,
Procavia capensis	ENSPCAG00000013476	1 retrocopy	retro_pcap_43,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus	ENSPVAG00000001666	1 retrocopy	retro_pvam_112,
Rattus norvegicus	ENSRNOG00000008212	1 retrocopy	retro_rnor_258,
Sus scrofa	ENSSSCG00000024912	1 retrocopy	retro_sscr_1 ,
Ictidomys tridecemlineatus	ENSSTOG00000015899	1 retrocopy	retro_itri_117,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,