RetrogeneDB ID: retro_mmul_1073

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:73299572..73300896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFRD2
• Ensembl ID: ENSMMUG00000020119
• Aliases: None
• Description: interferon-related developmental regulator 2 [Source:RefSeq peptide;Acc:NP_001253766]

Sequence

>retro_mmul_1073
ATGCCTCGCGCCCGTTACAGGCAACACGCTCCGGAAGGGTGGTCCGCGCCGTGGAGGAGGTGCCCGGAGCAGTACCCAAG
CTGACTCGGGTTGCAGTGATGATGAGGCAGCCAGTGAGGCCCGCAGCACCGCCAGTGAATGCCCCAGGCTTCTCAGCACC
ACTGCGGAGGACAGCCTTGTGGGGGATGTCGTGGATGAGCAGGGCCAGCAGGAAGACCTTGAGGAAAAGCTGAAGGAGTA
TGTGGACTGCCTCACAGACAAGAGTCCCAAGACCCGGCAGGGTGCTCTCAAGAGCCTGCGCCTGGCCCTGGCGTCGCGCC
TACTCCTCGACTTCTTGCTGGAGCGCCGCCTCGCACTAGCTGATGCCCTGGAAAAGTGCCTCAGGAAAGGGAAGGGAGAG
GAACAAGCCCTGGCTGCTGCTGTGCGAGGCCTGCTCTGCGTGCAGCTGGGCCCTGAACCCAAGGGTGAGGAGCTGTTCCA
CAGCCTGCAGCCTCTGCTGGTCTCTATGCTCAGTGACAGCACAGCTAGCCCTGCTGCCAGGCTCCACTGTGCTTCTGCTC
TTGGCCTGGGCTGCTACGTGGCTGCTGCCGACATCCAGGACCTAGTCTCTTGCCTTGCCTGCTTAGAAAGTGTTTTCAGC
CGGTTCTATGGCTTGGGTAGCTCCACGACTCCTGTGGTTCCTGCCAGCCTGCACGGCCTGCTCTGTGCTGCCCTGCAGAC
CTGGGCATTGCTGCTCACCATCTTCCCCAGCACCCAAATCAGCCACATCCTTGACAGGCAGCTGCCCCGGCTGCCCCAGC
TCTTGTCCAGTTAAAGTGTGAACCTGTGGATCGCTGCCGGTGAAACCATTGCACTGCTCTTTGAGCTTGCCCGGGACCTT
GAGGAGGTGTTTGTTTACGAGGACATGGAGGCCCTCTGCAGTGTCCTGCGCACTCTGGCCACTGACAGTAACAAGTACCG
TGCCAAGGCCGATCGCCAGCGCCAGGGCTCTACTTTCCGCGCCGTGCTGCACTCGGTGGAGGGCGGTGAACGTGAAGAAG
AGATAGTGCGCTTCGGCTTTGAGGTGCTCTACAGGGACAGCTGGGCTGGGCACCGGATCTACACTGCCTTCAAGGAAGTG
CTGGGTTCAGCTATGCACCACCACCTCCGGAGCAATGAGCTACTCCGTGACATCTTTGGCCTGGGCCCTGTGCTGGTGCT
GGATGCCACTGCCCTGAAGGCCTGCAAGGTTCCACGCTTCGAGAAGCACCTGTACAATACTGCCACCTTCAAAGCCCGGA
CCAAGGCTCGAAGCCGTGTGCGGAGCAAGCGGGCAGACATCCTG

Alignment

ORF - retro_mmul_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPRAR-KGNTLRKGGQRRGGGARSSAQADSGSSDDEAASEARSTTSECPSLLSTTAEDSLGGDVVNEQGQ
          MPRAR..GNTLRKGG.RRGGGARSS.QADSG.SDDEAASEARST.SECP.LLSTTAEDSL.GDVV.EQGQ
Retrocopy MPRAR>TGNTLRKGGPRRGGGARSSTQADSGCSDDEAASEARSTASECPRLLSTTAEDSLVGDVVDEQGQ

Parental  QEDLEEKLKEYVDCLTDKSAKTRQGALESLRLALASRLLPDFLLERRLTLADALEKCLKKGKGEEQALAA
          QEDLEEKLKEYVDCLTDKS.KTRQGAL.SLRLALASRLL.DFLLERRL.LADALEKCL.KGKGEEQALAA
Retrocopy QEDLEEKLKEYVDCLTDKSPKTRQGALKSLRLALASRLLLDFLLERRLALADALEKCLRKGKGEEQALAA

Parental  AVLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCASALGLGCYVAAADIQDLVSCLACLE
          AV.GLLCVQLGP.PKGEELFHSLQPLLVS.LSDSTASPAA.LHCASALGLGCYVAAADIQDLVSCLACLE
Retrocopy AVRGLLCVQLGPEPKGEELFHSLQPLLVSMLSDSTASPAARLHCASALGLGCYVAAADIQDLVSCLACLE

Parental  SVFSRFYGLGSSTTPVVPASLHGLLCAALQAWALLLTICPSTQISHILDRQLPRLPQLLSSESVNLRIAA
          SVFSRFYGLGSSTTPVVPASLHGLLCAALQ.WALLLTI.PSTQISHILDRQLPRLPQLLSS.SVNL.IAA
Retrocopy SVFSRFYGLGSSTTPVVPASLHGLLCAALQTWALLLTIFPSTQISHILDRQLPRLPQLLSS*SVNLWIAA

Parental  GETIALLFELARDLEEEFVYEDMEALCSVLRTLATDSNKYRAKADRRRQRSTFRAVLHSVEGGECEEEIV
          GETIALLFELARDLEE.FVYEDMEALCSVLRTLATDSNKYRAKADR.RQ.STFRAVLHSVEGGE.EEEIV
Retrocopy GETIALLFELARDLEEVFVYEDMEALCSVLRTLATDSNKYRAKADRQRQGSTFRAVLHSVEGGEREEEIV

Parental  RFGFEVLYMDSWARHRIYTAFKEVLGSGMHHHLQNNELLRDIFGLGPVLVLDATALKACKVPRFEKHLYN
          RFGFEVLY.DSWA.HRIYTAFKEVLGS.MHHHL..NELLRDIFGLGPVLVLDATALKACKVPRFEKHLYN
Retrocopy RFGFEVLYRDSWAGHRIYTAFKEVLGSAMHHHLRSNELLRDIFGLGPVLVLDATALKACKVPRFEKHLYN

Parental  AAAFKARTKARSRVRDKRADIL
          .A.FKARTKARSRVR.KRADIL
Retrocopy TATFKARTKARSRVRSKRADIL

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
SRP007412_brain	0.00 RPM	5.49 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.98 RPM
SRP007412_cerebellum	0.00 RPM	5.42 RPM
SRP007412_heart	0.00 RPM	15.78 RPM
SRP007412_kidney	0.00 RPM	11.03 RPM
SRP007412_liver	0.08 RPM	45.40 RPM
SRP007412_testis	0.08 RPM	10.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1073 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1073 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1073 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
Callithrix jacchus	ENSCJAG00000004993	1 retrocopy	retro_cjac_4213,
Macaca mulatta	ENSMMUG00000020119	1 retrocopy	retro_mmul_1073 ,
Otolemur garnettii	ENSOGAG00000012534	1 retrocopy	retro_ogar_2236,
Sus scrofa	ENSSSCG00000024363	1 retrocopy	retro_sscr_445,