RetrogeneDB ID: retro_sscr_387

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:148678456..148679020(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSSSCG00000007609
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_sscr_387
AGTCAGAAGGATGGAGTCTGGAAGCTAACCTTGGTGACACTGAGAATCAAGTAAGCCTCTTTTGTGAAGTGGTCTCCTCT
AAAGAACAAATTTGCTATGGATAATGAAAAACAATTCACTTCCATCTGTCACTTGAGTATAAAGATGACAAGTAGGTAAG
CAAGGACATTAAAAAGCCAGTTCATTCAACTATTCTTAGTTTGGATCGGTATCTCAATAGTGTCTCACTGGCAGCAGGAT
TATGAGACTTCAAATGCAGATTAAGTACTTCTGCATATAATTATAAAGTGGATGAAAGGCCAACCAGTATGCCATGGAGC
AGCAAGGTACCTTTTAGTTAGCTGATGTCAGAGTTTTGTGGCACTGGAAGCTGGGTCCCAGGTTCACCTTCTCTGCCAGT
GGGAGCTCTCTGGCCTGGGTCAGCCATGACAGCACTATGTCCAGTGCTGGTATCTCAAACAGTATTCAGGTTTGAATCTG
AAAACAAAGTTCCTGCCACTCCTGAGCTTATTACATCTCCCAGAGAATGGTGCTGCTGGCCATGAATGCTGCCCGGTGCT
CTTT

Alignment

ORF - retro_sscr_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.91 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYF-ESENDWWVSKHIKKPIRSTVLSL
          SQKDGVWK.TLV.LRI...A.FVKWSPL.NKFA........S.C...E...D..VSK.IKKP..ST.LSL
Retrocopy SQKDGVWKLTLVTLRI-K*ASFVKWSPLKNKFAMDNEKQFTSICHL<EYKDDK*VSKDIKKPVHSTILSL

Parental  DWHPNNVLLAAGSCDFKCRV-FSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHG-VSFSASG
          D...N.V.LAAG..DFKCR...SAY...VDE.P.S.PW.SK.PF..LMSEF...GTG.WV.G...FSASG
Retrocopy DRYLNSVSLAAGL*DFKCRLSTSAYNYKVDERPTSMPWSSKVPFS*LMSEF--CGTGSWVPG<FTFSASG

Parental  SRLAWVSHDSTVSVADASKSVQV-STLKTEFLPLLSVSFVSENSVVAAGHDCCPMLF
          S.LAWVSHDST.S.A..S.S.QV...LKT.FLPLLS.....EN...AAGH.CCP.LF
Retrocopy SSLAWVSHDSTMSSAGISNSIQV<LNLKTKFLPLLSLLHLPENG--AAGHECCPVLF

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	88.53 RPM
SRP014902_testis	0.00 RPM	98.73 RPM
SRP018288_heart	0.03 RPM	48.93 RPM
SRP018288_kidney	0.00 RPM	104.02 RPM
SRP018288_liver	0.00 RPM	38.86 RPM
SRP018288_lung	0.00 RPM	97.75 RPM
SRP018856_adipose	0.00 RPM	86.41 RPM
SRP035408_brain	0.19 RPM	51.93 RPM
SRP035408_liver	0.00 RPM	25.83 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_387 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005984	5 retrocopies	retro_dnov_1615, retro_dnov_1839, retro_dnov_1966, retro_dnov_2257, retro_dnov_941,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Sus scrofa	ENSSSCG00000007609	1 retrocopy	retro_sscr_387 ,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,
Tursiops truncatus	ENSTTRG00000003002	4 retrocopies	retro_ttru_1621, retro_ttru_1838, retro_ttru_575, retro_ttru_853,