RetrogeneDB ID: retro_mmul_1982

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:142660581..142661467(-)
• Located in intron of: ENSMMUG00000002212

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEIL2
• Ensembl ID: ENSMMUG00000019209
• Aliases: None
• Description: None

Sequence

>retro_mmul_1982
CTGCAGTCTCTGTGGCTCCAGGACACCCAGGTCCATGGAAAGAAATTATTCCTTAGATGTGATCCAGGTGAAGAAATGGG
GCCTGCTGGCAACAGCCCACCGCCAGAGCCTCCACGGAAAGAAACGCAGAAGAAAGGGACTGTGGACCCAAAGCAGGCCC
GGGAGCCCACTGGGCAGAAGACCCTTGATGCCTTCTCACTGTCCGCAGAACTCGTCCCCCGGGGAGAGGATGATTACAAA
TGTTTGGAAGGAGACACACCTGCCGGAGATGCTGGGAGGTGGCTGCGTGTCAGCTCTTGTTTGTTTGGCAGCATTTGGGT
GAACGATTTCTCCAGAACTAAGAAAGCCAGCAAGAGCGGGTACTGGAGGGAACCTGCCCCGAGGTTGGTCCTGTACTTTG
GTGGTGGTGGTTTCCTGGCATATTATAATCGTCAGATGTCTTGGAGCTCTTCCCCAGAGGTCACACCCACCTGTGACATC
CTGTCTGAGAAGTTCCATTGAGGACAAGCCTTGGAAGCTGTAGGCCAGGCTCAACCTGTCTGCTATACACCGTTGGACCA
GAAATACTTCTCAGGGCTAGGAAACATCATTAAGAATGAAGTCTTATACAGAGCTGGCATCCATCCCCTTTCTCTTGGTT
CAGTCCTGAGTGCCTCCATGTCAGGAGGCCCTGGTGGATCACATGGTAGAGTTCAGTACAGGCTGGCTGCAGGGCAAGTT
CCAGAGCAAACCGCAGCACATGCAGGTCTACCAGAAAGAACAGTGCCTTGCTGGCCACCAGGTCATAAAGAAGCCATTTG
GGCCTTCAGGAGGGTTCCAGAGGCTCACCTGGTGGTGCCCACAATGCCAGCCTCAGTTGTCAGAGTAGCCAGAACAGCGC
CAGTTC

Alignment

ORF - retro_mmul_1982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.41 %
• Parental protein coverage: 88.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQSLWLQDTQVHGKKLFLRFDPDKEMEAPGSSPPPEPPQKEAQKEGAADPKQAGEPSGQKTPDGSSQSAE
          LQSLWLQDTQVHGKKLFLR.DP..EM...G.SPPPEPP.KE.QK.G..DPKQA.EP.GQKT.D..S.SAE
Retrocopy LQSLWLQDTQVHGKKLFLRCDPGEEMGPAGNSPPPEPPRKETQKKGTVDPKQAREPTGQKTLDAFSLSAE

Parental  LNPQGEDESECLEGDAPAGDAGRWLRVSFGLFGSVWVNEFSRAKKANKRGDWRDPSPRLVLYFGGGGFLA
          L.P.GED...CLEGD.PAGDAGRWLRVS..LFGS.WVN.FSR.KKA.K.G.WR.P.PRLVLYFGGGGFLA
Retrocopy LVPRGEDDYKCLEGDTPAGDAGRWLRVSSCLFGSIWVNDFSRTKKASKSGYWREPAPRLVLYFGGGGFLA

Parental  FYNCQMSWSSSPVVTPACDILSEKFHRGQALEALGQAQPVCYTLLDQRYFSGLGNIIKNEVLYRAGIHPL
          .YN.QMSWSSSP.VTP.CDILSEKFH.GQALEA.GQAQPVCYT.LDQ.YFSGLGNIIKNEVLYRAGIHPL
Retrocopy YYNRQMSWSSSPEVTPTCDILSEKFH*GQALEAVGQAQPVCYTPLDQKYFSGLGNIIKNEVLYRAGIHPL

Parental  SLGSALSA-PRREALVDHVVEFSTAWLQGKFQGRPQHTQVYQKEQCPAGHQVMKEAFGPPGGFQRVTWWC
          SLGS.LSA.P..EALVDH.VEFST.WLQGKFQ..PQH.QVYQKEQC.AGHQV.K..FGP.GGFQR.TWWC
Retrocopy SLGSVLSA>PCQEALVDHMVEFSTGWLQGKFQSKPQHMQVYQKEQCLAGHQVIKKPFGPSGGFQRLTWWC

Parental  PQCQPQLSEEPEQRQF
          PQCQPQLSE.PEQRQF
Retrocopy PQCQPQLSE*PEQRQF

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	5.94 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.17 RPM
SRP007412_cerebellum	0.00 RPM	7.23 RPM
SRP007412_heart	0.00 RPM	2.36 RPM
SRP007412_kidney	0.12 RPM	2.11 RPM
SRP007412_liver	0.00 RPM	6.33 RPM
SRP007412_testis	0.00 RPM	1.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1982 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1982 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1982 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3111
Pan troglodytes	retro_ptro_2103
Pongo abelii	retro_pabe_2569

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154328	1 retrocopy	retro_hsap_3111,
Macaca mulatta	ENSMMUG00000019209	1 retrocopy	retro_mmul_1982 ,
Nomascus leucogenys	ENSNLEG00000015054	1 retrocopy	retro_nleu_766,
Pongo abelii	ENSPPYG00000018348	1 retrocopy	retro_pabe_2569,
Pan troglodytes	ENSPTRG00000019995	1 retrocopy	retro_ptro_2103,