RetrogeneDB ID: retro_sscr_748

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:14783033..14783276(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSSSCG00000002307
• Aliases: None
• Description: Sus scrofa enhancer of rudimentary homolog (Drosophila) (ERH), mRNA. [Source:RefSeq mRNA;Acc:NM_001185163]

Sequence

>retro_sscr_748
ATTTTGCGGGCACAGCCCAGCAAGGGGCCGGAAGGCAGAGCTTAGGCTGACCATGAACCTGTACATGAATGCAGGGAAGG
CAATTATAAAATGGAGGAAGAACATCTGAAGAAGATGAACCCCAACAGCCCCTCTATCGCACGTGGCATCAGCCCGTTGT
TTGCTTTTATGGATGACCTGGCAGACCCCATCTGTCTTGTTTACTGAGCAGATACCCAGACACACCAGCCTTATGACAAA
GAC

Alignment

ORF - retro_sscr_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 77.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCLVYRA
          IL..QP.K.PEGR..AD.E.V.EC.EG..KM.EEHLK.MNPNSPSI...IS.LF.F.DDLAD..CLVY.A
Retrocopy ILRAQPSKGPEGRA*ADHEPVHECREGNYKMEEEHLKKMNPNSPSIARGISPLFAFMDDLADPICLVY*A

Parental  DTQTYQPYNKD
          DTQT.QPY.KD
Retrocopy DTQTHQPYDKD

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	39.69 RPM
SRP014902_testis	0.00 RPM	54.32 RPM
SRP018288_heart	0.00 RPM	29.10 RPM
SRP018288_kidney	0.10 RPM	75.36 RPM
SRP018288_liver	0.00 RPM	57.89 RPM
SRP018288_lung	0.00 RPM	37.68 RPM
SRP018856_adipose	0.00 RPM	51.91 RPM
SRP035408_brain	0.00 RPM	142.83 RPM
SRP035408_liver	0.00 RPM	129.75 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_748 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_748 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017798	4 retrocopies	retro_btau_1260, retro_btau_438, retro_btau_651, retro_btau_795,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Erinaceus europaeus	ENSEEUG00000007758	6 retrocopies	retro_eeur_105, retro_eeur_108, retro_eeur_115, retro_eeur_116, retro_eeur_185, retro_eeur_546,
Echinops telfairi	ENSETEG00000016172	5 retrocopies	retro_etel_1122, retro_etel_1451, retro_etel_715, retro_etel_716, retro_etel_975,
Homo sapiens	ENSG00000100632	2 retrocopies	retro_hsap_3594, retro_hsap_3799,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Ochotona princeps	ENSOPRG00000000086	2 retrocopies	retro_opri_1140, retro_opri_519,
Pongo abelii	ENSPPYG00000005939	2 retrocopies	retro_pabe_2954, retro_pabe_3104,
Sus scrofa	ENSSSCG00000002307	1 retrocopy	retro_sscr_748 ,