RetrogeneDB ID: retro_rnor_524

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:210449129..210449532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mospd3
• Ensembl ID: ENSRNOG00000001396
• Aliases: None
• Description: motile sperm domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001020800]

Sequence

>retro_rnor_524
GGGCCGTGGGATGCCCCTCCTTGCTCAGGACCCATTATCAGGGTGCTGAACTTTCCCCAGATCTAGCACTCAGGGCTTAT
CGAAGGAGTGGTCCCTGGAGCTGCCAACCCTCTACAACCACATGGGACCTGTGCTCTGCTTCCAAGTCCTGTGTACAACA
CCTGCCAAGCGTACGGTATTTGATATAGAAGGTTATGTGAAGCCTCAGTCTTACATTGACATAAGATTTGACATTTGACC
CCCATCCCTAACCACAGTGATGTCCAGATCTGACTCTGCATTGAGCTGTTTGAGGAGGCAGGGTAAGGGATTAGTAGTCA
GATAAAAAGACATCATGTCTGTTCTTTGGGCTCCAGAGTACCCATTTGAGCTTCGTAGACATTCTGAGGCAAACCCAGGC
CCT

Alignment

ORF - retro_rnor_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.99 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSRGSPPSSGPVVPVLVFP-PDLVFRADQRSGP-RQLLTLYNPTGTALRFRVLCTAPAKYTVFDAEGYVK
          G....PP.SGP...VL.FP.PDL..RA..RSGP...L.TLYN..G..L.F.VLCT.PAK.TVFD.EGYVK
Retrocopy GPWDAPPCSGPIIRVLNFP<PDLALRAYRRSGP<LELPTLYNHMGPVLCFQVLCTTPAKRTVFDIEGYVK

Parental  PQSCIDI-VIRHVAPIPSHYDVQDRFRIELSEEG-AEGRVVGRKDVTSVLRAPAYPLELQGHSEPTPNP
          PQS.IDI..I.H..PIP.H.DVQ....IEL.EE....G.VV..KD..SVL.AP.YP.EL..HSE..P.P
Retrocopy PQSYIDI<KI*HLTPIPNHSDVQI*LCIELFEEA>GKGLVVR*KDIMSVLWAPEYPFELRRHSEANPGP

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
SRP017611_brain	0.00 RPM	13.59 RPM
SRP017611_kidney	0.00 RPM	17.31 RPM
SRP017611_liver	0.00 RPM	37.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_524 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_524 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026246	1 retrocopy	retro_btau_1854,
Myotis lucifugus	ENSMLUG00000010017	1 retrocopy	retro_mluc_1956,
Oryctolagus cuniculus	ENSOCUG00000005694	1 retrocopy	retro_ocun_181,
Rattus norvegicus	ENSRNOG00000001396	1 retrocopy	retro_rnor_524 ,