RetrogeneDB ID: retro_sscr_1129

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: JH118666.1:4104..4476(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000010492
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MCFD2
• Ensembl ID: ENSSSCG00000021325
• Aliases: None
• Description: multiple coagulation factor deficiency 2 [Source:HGNC Symbol;Acc:18451]

Sequence

>retro_sscr_1129
GCCAGGGCCAAGGTGGCAGGAGCCAGCTTATCCCATCCTGCAGCGTGGGTCTGGATAAGAACACAATGCAGGATCAAGAG
CATATCACGGAGCATCCAGAAGGTGGCACTGACAAACCAGAGGTTGAGCTGTTCCTACAAGAACTGCAGCTCCACTATTT
CAAAATGCAATTATGACAGCAATCATCATTTGCTTGGTGGTCTAGAACTCTCCACAGCCATCGCTCATGTCCATGAGGAG
AAAGGAAATGAAGAGACACCACCAAGGAGGGAAGATGAACTGATCAACTTAATGGATGGTGTAGATGGTGTTTTGAGAGA
AAATGATAAGAACAATGATGGATATTTCGTTGTGTTCCCCAAATCACTGCAG

Alignment

ORF - retro_sscr_1129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.84 %
• Parental protein coverage: 80.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARAKEPGASFSHPG-SVGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQELQLHYFKM-HDYDGNNLLDGL
          ARAK..GAS.SHP..SVGLDKNT..DQEHI.EH.EG...KPE.E...QELQLHYFKM........LL.GL
Retrocopy ARAKVAGASLSHPA<SVGLDKNTMQDQEHITEHPEGGTDKPEVELFLQELQLHYFKM>NYDSNHHLLGGL

Parental  ELSTAITHVHKEEGNEQA-PMSEDELINLIDGV---LRDDDKNNDGYIDYAEFAKSLQ
          ELSTAI.HVH.E.GNE...P..EDELINL.DGV...LR..DKNNDGY.....F.KSLQ
Retrocopy ELSTAIAHVHEEKGNEETPPRREDELINLMDGVDGVLRENDKNNDGY--FVVFPKSLQ

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	53.36 RPM
SRP014902_testis	0.00 RPM	48.94 RPM
SRP018288_heart	0.00 RPM	163.42 RPM
SRP018288_kidney	0.00 RPM	137.51 RPM
SRP018288_liver	0.00 RPM	180.86 RPM
SRP018288_lung	0.00 RPM	90.12 RPM
SRP018856_adipose	0.00 RPM	120.04 RPM
SRP035408_brain	0.00 RPM	45.00 RPM
SRP035408_liver	0.00 RPM	298.90 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1129 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1129 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006097	2 retrocopies	retro_amel_720, retro_amel_906,
Canis familiaris	ENSCAFG00000032480	1 retrocopy	retro_cfam_797,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840, retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Mustela putorius furo	ENSMPUG00000012043	1 retrocopy	retro_mputfur_885,
Sus scrofa	ENSSSCG00000021325	2 retrocopies	retro_sscr_1129 , retro_sscr_422,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118,
Vicugna pacos	ENSVPAG00000010692	1 retrocopy	retro_vpac_368,