RetrogeneDB ID: retro_sscr_947

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:95025844..95026295(-)
• Located in intron of: ENSSSCG00000002275

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXI1
• Ensembl ID: ENSSSCG00000022128
• Aliases: None
• Description: MAX interactor 1, dimerization protein [Source:HGNC Symbol;Acc:7534]

Sequence

>retro_sscr_947
CGACAAGCTCATTTTTGCCTGCGTTTAGAAGGCTTAAAAATTCTGATTCCACTAAGAACAGATCGCACCAGGCCCACAGC
ACTTGGTTTGCTCAACAAAGCCAAAGCACACATCGAGCAACTTGAAGAAGTTGAGAGGAAGAGCCAACAACCAGCTAGAG
AACTTGGAATGAGGACAGAGATTTTTAAAGCAACCACTGGAACAGCTGCAGGGTCCTCAGGAGATGGAACAAATACAAAT
GGACAGCATTGGATCAACTATTTCTTCAGATCATTCAGATTCAGCGCAAGAGGAGATTGAAGTGGATGTTGAAAGCACAG
AGTTCTCCTATGGAGAAGTGGACAATATCAGTACCACCATCATCAGTGACACTGATGACAACAGCAGCCTGCAGAGTAGT
GGAAGTGACAAGGGTTACTCCGGTGCCAGGGTCAAAGTTTCGTTCACTTCC

Alignment

ORF - retro_sscr_947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRAHLRLCLERLKVLIPLGPDCTRHTTLGLLNKAKAHIKKLEEAERKSQ-HQLENLEREQRFLKRRLEQL
          R.AH..L.LE.LK.LIPL..D.TR.T.LGLLNKAKAHI..LEE.ERKSQ..QLENLE..QRFLK..LEQL
Retrocopy RQAHFCLRLEGLKILIPLRTDRTRPTALGLLNKAKAHIEQLEEVERKSQ>NQLENLE*GQRFLKQPLEQL

Parental  QGPQEMERIRMDSIGSTISSDRSDSEREEIEVDVESTEFSHGEVDNISTTSISDIDDHSSLQSIGSDEGY
          QGPQEME.I.MDSIGSTISSD.SDS..EEIEVDVESTEFS.GEVDNISTT.ISD.DD.SSLQS.GSD.GY
Retrocopy QGPQEMEQIQMDSIGSTISSDHSDSAQEEIEVDVESTEFSYGEVDNISTTIISDTDDNSSLQSSGSDKGY

Parental  SSASVKLSFTS
          S.A.VK.SFTS
Retrocopy SGARVKVSFTS

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	12.21 RPM
SRP014902_testis	0.85 RPM	26.31 RPM
SRP018288_heart	0.16 RPM	38.85 RPM
SRP018288_kidney	0.00 RPM	14.28 RPM
SRP018288_liver	0.00 RPM	20.47 RPM
SRP018288_lung	0.00 RPM	43.38 RPM
SRP018856_adipose	0.00 RPM	23.62 RPM
SRP035408_brain	0.00 RPM	32.30 RPM
SRP035408_liver	0.00 RPM	16.82 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_947 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948,
Sus scrofa	ENSSSCG00000022128	1 retrocopy	retro_sscr_947 ,