RetrogeneDB ID: retro_sscr_105

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:41526545..41526921(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf45
• Ensembl ID: ENSSSCG00000027792
• Aliases: None
• Description: chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628]

Sequence

>retro_sscr_105
ATGGAGGTCCAGCCTGAGCCCCAGTTTGGCCCCACCAGTTCATCATCTTCCGGGGACTGCTCCGGGGTCTTGGTGTCCAA
GGAGTTGCTGATGGCAGAGAGCAGCGGCCAAGGAGGGAAATGGGACAGGTTGCTCATCAACTCCAAGACTACTTCCAGGA
GGAATTCCACTCTTTAAACATTTCCGATGGAGAGGAGTCCCTTCTTGGACCAAGGACAGACCTTTCTCTCACAGATAGTC
AGGCATGAACAGCTGAGAAAAGAAATGGCAGCTGCACCCACCACCTGGTCGTTTCAATATTGAAAATACTGATGAGATTC
TTGGAAAAGCTAAATAAATGGATGTGGCCTCCTTTGAGATGAATCTGCCTGACTCA

Alignment

ORF - retro_sscr_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 68.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEVQSESQSGPTCSSSSQNHSGVSVSKELLTAGSGDQGGIWDKLLINSKPNSRKNSTLQTVRIERSPLLD
          MEVQ.E.Q.GPT.SSSS...SGV.VSKELL.A.S..QGG.WD.LLINSK..SR.NSTL.T...ERSP.LD
Retrocopy MEVQPEPQFGPTSSSSSGDCSGVLVSKELLMAESSGQGGKWDRLLINSKTTSRRNSTL*TFPMERSPFLD

Parental  RVQTFLPQMAQANEQLRKEMAAA-PPGCFNIENIDETLGKVIQMDVALFEMNPSDS
          ..QTFL.Q............AA..PPG.FNIEN.DE.LGK...MDVA.FEMN..DS
Retrocopy QGQTFLSQIVRHEQLRKEMAAAP>PPGRFNIENTDEILGKAK*MDVASFEMNLPDS

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	1.86 RPM
SRP014902_testis	0.00 RPM	7.07 RPM
SRP018288_heart	0.00 RPM	4.56 RPM
SRP018288_kidney	0.00 RPM	5.81 RPM
SRP018288_liver	0.00 RPM	10.87 RPM
SRP018288_lung	0.00 RPM	3.46 RPM
SRP018856_adipose	0.00 RPM	11.60 RPM
SRP035408_brain	0.00 RPM	4.80 RPM
SRP035408_liver	0.00 RPM	8.22 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_105 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_105 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014728	1 retrocopy	retro_cjac_333,
Dasypus novemcinctus	ENSDNOG00000017235	1 retrocopy	retro_dnov_2327,
Homo sapiens	ENSG00000151131	1 retrocopy	retro_hsap_292,
Gallus gallus	ENSGALG00000012694	1 retrocopy	retro_ggal_15,
Gorilla gorilla	ENSGGOG00000027272	1 retrocopy	retro_ggor_331,
Macaca mulatta	ENSMMUG00000017133	1 retrocopy	retro_mmul_551,
Nomascus leucogenys	ENSNLEG00000006584	1 retrocopy	retro_nleu_2414,
Pongo abelii	ENSPPYG00000004897	1 retrocopy	retro_pabe_382,
Pan troglodytes	ENSPTRG00000005381	1 retrocopy	retro_ptro_240,
Sus scrofa	ENSSSCG00000027792	2 retrocopies	retro_sscr_105 , retro_sscr_153,
Tursiops truncatus	ENSTTRG00000005714	1 retrocopy	retro_ttru_1381,