RetrogeneDB ID: retro_sscr_487

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:8655902..8656252(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA5
• Ensembl ID: ENSSSCG00000004283
• Aliases: None
• Description: developmental pluripotency associated 5 [Source:HGNC Symbol;Acc:19201]

Sequence

>retro_sscr_487
ATGGGGAGGCTGAGGGTTCAGAATGACATTGCACCTTGGGTGGGAGCTCCCAAAGACTTTAAAGTGGCTGAAGTGTTTCA
GGTCTAGACGTGGCTGCTGGAAACCTTATTTGCCCAGAAGGCTCTCAAACCCCGCACATCGTCGAGCAGATGAGAAAAGT
CATGCTCGGAGTAAAGGCTCTGGAATCTTCAGAACACACCAAAGTTAGGGTTTACGACCCTTACTTGTACAGGTTCCAGA
CTAAGTGGACATTCTAGTCCATGGCCGAGTGGCACCGCCAGCAGCAGGAATGCGGGATGCTCCAACTTGAGTAAGCCATG
AATTCACTAGAGCCAGGTCCTTGGATGAAG

Alignment

ORF - retro_sscr_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKLPPKPNDILSWVGAPEDFTEPEVFQVQTRLLEALFG-PEGSRIPY-VEKVSKVMLEMKALESSDLTE
          MG.L....NDI..WVGAP.DF...EVFQV.T.LLE.LF..PEGS..P..VE...KVML..KALESS..T.
Retrocopy MGRLRVQ-NDIAPWVGAPKDFKVAEVFQV*TWLLETLFA<PEGSQTPHIVEQMRKVMLGVKALESSEHTK

Parental  VMVYGPYLYKFRTKWMLQSMAEWHCQRQERGMRRLEEAMNSLELCPPMK
          V.VY.PYLY.F.TKW...SMAEWH.Q.QE.GM..LE.AMNSLE..P.MK
Retrocopy VRVYDPYLYRFQTKWTF*SMAEWHRQQQECGMLQLE*AMNSLEPGPWMK

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	0.13 RPM
SRP014902_testis	0.00 RPM	0.14 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.10 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.25 RPM
SRP035408_liver	0.00 RPM	0.12 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_487 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002647	2 retrocopies	retro_cfam_1216, retro_cfam_524,
Choloepus hoffmanni	ENSCHOG00000012338	1 retrocopy	retro_chof_2495,
Callithrix jacchus	ENSCJAG00000009945	3 retrocopies	retro_cjac_1978, retro_cjac_62, retro_cjac_85,
Dasypus novemcinctus	ENSDNOG00000011544	4 retrocopies	retro_dnov_115, retro_dnov_15, retro_dnov_2318, retro_dnov_53,
Dipodomys ordii	ENSDORG00000000378	2 retrocopies	retro_dord_324, retro_dord_690,
Homo sapiens	ENSG00000203909	1 retrocopy	retro_hsap_2067,
Gorilla gorilla	ENSGGOG00000012001	1 retrocopy	retro_ggor_1489,
Myotis lucifugus	ENSMLUG00000004463	1 retrocopy	retro_mluc_1051,
Macaca mulatta	ENSMMUG00000000417	1 retrocopy	retro_mmul_1409,
Mus musculus	ENSMUSG00000060461	7 retrocopies	retro_mmus_127, retro_mmus_1280, retro_mmus_1537, retro_mmus_1666, retro_mmus_2557, retro_mmus_3415, retro_mmus_58,
Pongo abelii	ENSPPYG00000016771	1 retrocopy	retro_pabe_1680,
Pan troglodytes	ENSPTRG00000029547	1 retrocopy	retro_ptro_1380,
Rattus norvegicus	ENSRNOG00000000199	3 retrocopies	retro_rnor_106, retro_rnor_28, retro_rnor_76,
Sus scrofa	ENSSSCG00000004283	2 retrocopies	retro_sscr_190, retro_sscr_487 ,
Ictidomys tridecemlineatus	ENSSTOG00000005326	2 retrocopies	retro_itri_199, retro_itri_703,