RetrogeneDB ID: retro_sscr_412

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:42342332..42342673(+)
• Located in intron of: ENSSSCG00000009890

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000022859
• Aliases: None
• Description: None

Sequence

>retro_sscr_412
CATAAGACTGGCAAACCCCTCACAATTTCTTGAAAGTGACAAGATACTATGGCTCTCTGTGGCTACGCTTCATCCTTGCA
TCCAGACTCATGGCAATTATTGTTTTGGCCCCCATGACCTCAAAGGACTTGCTGATGGCAAGTCCTGAAAACTGTTACAC
CTCAGCCAAGGGCTGCACTGCCACCTTGGGCAACTTTGCCAAGGCCACTTTTGATGCTACCTCTAAAACCTACTGCTATC
TTACTTCTGACCTCTGGAAGGGGACTATGCTAACCATGGTTCCCTAACAGGAATTCACTGACTATCTTGTAAAGATCCAC
ACCAGAGTCTCTGTGCAGAAA

Alignment

ORF - retro_sscr_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.61 %
• Parental protein coverage: 61.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKIGKPHTVP-CKVTGRCGSVLVRLIPAPRGTGI-VSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKA
          .K.GKP.T....KVT...GS...R.I.A.R...I.V.AP...K.L.MA....CYTSA.GCTATLGNFAKA
Retrocopy HKTGKPLTIS<LKVTRYYGSLWLRFILASRLMAIIVLAPMTSKDLLMASPENCYTSAKGCTATLGNFAKA

Parental  TFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQR
          TFDA.SKTY.YLT.DLWK.T..T..P.QEFTD.LVK.HTRVSVQ.
Retrocopy TFDATSKTYCYLTSDLWKGTMLTMVP*QEFTDYLVKIHTRVSVQK

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	0.27 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.05 RPM	0.50 RPM
SRP018288_kidney	0.20 RPM	0.49 RPM
SRP018288_liver	0.16 RPM	0.32 RPM
SRP018288_lung	0.10 RPM	0.31 RPM
SRP018856_adipose	0.15 RPM	0.48 RPM
SRP035408_brain	0.06 RPM	0.06 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_412 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_412 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Choloepus hoffmanni	ENSCHOG00000012360	9 retrocopies	retro_chof_1056, retro_chof_2398, retro_chof_2545, retro_chof_2607, retro_chof_368, retro_chof_378, retro_chof_535, retro_chof_919, retro_chof_989,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Sus scrofa	ENSSSCG00000022859	8 retrocopies	retro_sscr_280, retro_sscr_293, retro_sscr_412 , retro_sscr_486, retro_sscr_729, retro_sscr_803, retro_sscr_950, retro_sscr_951,