RetrogeneDB ID: retro_sscr_1149

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:34372767..34373098(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030863
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFB2
• Ensembl ID: ENSSSCG00000016495
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7697]

Sequence

>retro_sscr_1149
CTGGCTGGCATGTCAGCTCTGAAGCAGCTGGTGGCCTTTTGTGTGCCGTGGAGGCCATTTCTTTAGAGGCCACCACGCGG
TGGCAGCTGGAGGCGGTGAAGTCTGTCATGCTGGTGGAAGTGTGCATATAGAGCCCTGGTACAGGTACAGACAGTTTCCC
CAGCGGACCAGATACCAGGTGATCCAGGCCAAGTTCTTCAGTGCAGCCACATGGTTCTGAATTCTCTGGCACTTTTGGCA
TGACTCAGATTCTGTGCTGGGTCACTTTCCACATCCAGGTCCTTCTCAGTGGACGGATGAAGAATTCGGTATCTTTTCTG
ATGATGAAAAC

Alignment

ORF - retro_sscr_1149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAGMSPLQRLA-PFTRVGGRFLRGRGAGVAGGGGVRHAGGGVHIEP--RYRQFPQLTRSQLIQAEFFSAT
          LAGMS.L..L..PF...GG.F.RG..A..AGGG.V.HAGG.VHIEP..RYRQFPQ.TR.Q.IQA.FFSA.
Retrocopy LAGMSALKQLV>PFVCRGGHFFRGHHAVAAGGGEVCHAGGSVHIEPWYRYRQFPQRTRYQVIQAKFFSAA

Parental  MWFWILWRFWHDSDAVLGHFPYPDPSQWTDEELGILPDDED
          .WF.ILW.FWHDSD.VLGHFP.P.PSQWTDEE.GI..DDE.
Retrocopy TWF*ILWHFWHDSDSVLGHFPHPGPSQWTDEEFGIFSDDEN

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	33.71 RPM
SRP014902_testis	0.00 RPM	32.96 RPM
SRP018288_heart	0.00 RPM	88.59 RPM
SRP018288_kidney	0.00 RPM	68.86 RPM
SRP018288_liver	0.00 RPM	25.59 RPM
SRP018288_lung	0.00 RPM	5.60 RPM
SRP018856_adipose	0.00 RPM	35.41 RPM
SRP035408_brain	0.00 RPM	22.23 RPM
SRP035408_liver	0.00 RPM	18.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1149 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1149 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149 ,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,