RetrogeneDB ID: retro_sscr_56

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:2371716..2372697(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000026323
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM50A
• Ensembl ID: ENSSSCG00000025303
• Aliases: None
• Description: family with sequence similarity 50, member A [Source:HGNC Symbol;Acc:18786]

Sequence

>retro_sscr_56
ATGGCTCAGTACAAGGGCACCATGCGCGAGGCGGGCCGGGCCCTGCACCTGCTCAAGAAGCGGGAGAAGCAGAAGGAGCA
GATGGAGGTGCTGAAGCAGCGCATCGCCGAGGAGACCATCAGCAAGTCCAAGGTGGACAAGAAGTTCTCGGCCCACTACG
ACGCGGTGGAGGCCGAGCTCAAGTCCAGCACCGTGGGGCTAGTGACCCTGAACGACATGAAGGCGCGGCAGGAGGCCCTG
GTGCGCGAGCGGGAGATGCAGCTGGCGCAGCGCGCGCGGCGGGAGAAGCGGCGGCGGCAGCTGGAGGCGCAGCGCGAGCG
GGAGCGCAAGCGCGAGCAGCGGCGCCAGATCTGCGGCCTGTCCTTCTCCACCGACGACGGCGACGACGACAGTGACGGGG
ACCGCGAGGCCGCCGAGCCCGCCGGGCCCCGGAGGCCCCTGGGCAAGGACCCGGCCGTGGACACCAGCTTCCTGCCGGAC
CGCGAGCGCGAGGAGGAGGAGCGGCGGCTGCGCGAGGAGCTGCGGCGCGAGTGGGAGGCGCGGCGCGAGCGCGTGAAGCG
CGAGGAGGTGGAGGTGACCTTCAGCTACTGGGACGGCTGCGGGCACCGGCGCGCCGCGCGCATCCACAAGGGCGGCACCG
TGCAGCAGTTCCTCAAGAGGGCGCTGCAGGCGCTGCGCCCCGACTTCCGCGAGCTGCGCGCGGCCGGCGTGGAGCAGCTG
CTGTTCGTCAAGGAGGACCTGATCCTGCCGCACTGCCACACCTTCTACGACCTGATCGTGGCGCAGGCGCGCGGCAAGAG
CGGGCCGCTCTTCACCTTCGACGTGCACGAAGACGTGCGGCTGCGCAGCGATGCCACCCTGGAGAAGGACAATTCGCACC
CGGGGCAAGGGGTGCTGCGCCACTGGTACAAAAAAAACAAGCACATCTTCCCCGCAGCCGCTGGGAACCCTACGAACCCC
AAGAAGCCCTGGGACCGCTAA

Alignment

ORF - retro_sscr_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.02 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EREEVTTKKRKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRT
          E..E.....R.LGK.P.VDTSFLPDR.REEEE.RLREELR.EWEA..E..K.EE.E.TFSYWDG.GHRR.
Retrocopy EAAEPAGPRRPLGKDPAVDTSFLPDREREEEERRLREELRREWEARRERVKREEVEVTFSYWDGCGHRRA

Parental  VKMKKGNTMQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLFNFDV
          ....KG.T.QQFL..AL..LR.DF.ELR.AGVEQL...KEDLI.PH.H.FYD.IV..ARGKSGPLF.FDV
Retrocopy ARIHKGGTVQQFLKRALQALRPDFRELRAAGVEQLLFVKEDLILPHCHTFYDLIVAQARGKSGPLFTFDV

Parental  HDDVRLLSDATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDK
          H.DVRL.SDAT.EKD.SH.G..VLR.WY.KNKHIFPA....P..P.K.WD.
Retrocopy HEDVRLRSDATLEKDNSHPGQGVLRHWYKKNKHIFPAAAGNPTNPKKPWDR

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	0.27 RPM	40.48 RPM
SRP014902_testis	0.42 RPM	40.88 RPM
SRP018288_heart	0.05 RPM	20.64 RPM
SRP018288_kidney	0.10 RPM	38.12 RPM
SRP018288_liver	0.00 RPM	22.55 RPM
SRP018288_lung	0.00 RPM	49.39 RPM
SRP018856_adipose	0.12 RPM	72.20 RPM
SRP035408_brain	0.25 RPM	98.01 RPM
SRP035408_liver	0.00 RPM	45.97 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_sscr_56 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CV869103	2371669	2372196	100	527	0	527

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_56 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_94
Mus musculus	retro_mmus_103

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56 ,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105, retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,