RetrogeneDB ID: retro_sscr_177

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:136455337..136455652(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSSSCG00000009821
• Aliases: None
• Description: Sus scrofa actin related protein 2/3 complex, subunit 3, 21kDa (ARPC3), mRNA. [Source:RefSeq mRNA;Acc:NM_001185135]

Sequence

>retro_sscr_177
TATATATAACTCTACATTTCTGATTGTCTAAAAAAAAAACTCCACAAGTGTAATTCTAAAAGCAAAGGTGAGAAATAATT
GTATACATTGGGGACCACTAATTTTCCCATTCCTGGAGAGCTTGGTTTTCCACTTAATGAAATTTATGCCAAACCTGCAA
ACAAACAGGAAGATGAATTGATGAGGGCCTAGTTACAACAGCTGAGGCAAGAGACTCGACTGAGACTTTGTGAGAAAGTT
TTTGACCCTCAGAATGAGAAACCCAGCAAGTGGTGGACTTGCTTTATGAAGAGACAATTCATGAACAAGTCTTTG

Alignment

ORF - retro_sscr_177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YITLYISECLKK-LQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQ
          YI.LYIS.C....L.KCNSKS.GEK..YTLG.TNFPIPGE.GFPLN.IYAKPANKQEDE.MRA.LQQLRQ
Retrocopy YI*LYISDCXXXXLHKCNSKSKGEK*LYTLGTTNFPIPGELGFPLNEIYAKPANKQEDELMRA*LQQLRQ

Parental  ETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSL
          ET.LRLCEKVFDPQN.KPSKWWTCF.KRQFMNKSL
Retrocopy ETRLRLCEKVFDPQNEKPSKWWTCFMKRQFMNKSL

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	44.73 RPM
SRP014902_testis	0.00 RPM	32.11 RPM
SRP018288_heart	0.05 RPM	40.76 RPM
SRP018288_kidney	0.00 RPM	106.48 RPM
SRP018288_liver	0.00 RPM	52.13 RPM
SRP018288_lung	0.00 RPM	125.96 RPM
SRP018856_adipose	0.00 RPM	49.98 RPM
SRP035408_brain	0.00 RPM	259.01 RPM
SRP035408_liver	0.00 RPM	117.95 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_177 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Homo sapiens	ENSG00000111229	5 retrocopies	retro_hsap_2431, retro_hsap_303, retro_hsap_3425, retro_hsap_892, retro_hsap_918,
Microcebus murinus	ENSMICG00000005485	2 retrocopies	retro_mmur_1009, retro_mmur_1507,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Mustela putorius furo	ENSMPUG00000002151	2 retrocopies	retro_mputfur_1346, retro_mputfur_1540,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Sus scrofa	ENSSSCG00000009821	1 retrocopy	retro_sscr_177 ,