RetrogeneDB ID: retro_mmul_1168

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:97956665..97957546(+)
• Located in intron of: ENSMMUG00000008629

Retrocopy information

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

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSMMUG00000002164
• Aliases: None
• Description: None

Sequence

>retro_mmul_1168
AAGAAATGTATTGCTTTTCCCACCAGCATTTCGGTAAATAACGGTGTATGTCACTTCTCCCCTTTGAAGAGCGGCCAGGA
TTACATTCTCAAGGAAGGTGACTTGGTAAAAATTGACCTTGGGGTCCATGCAGACGGCTTCACCGCTAATGTAGCTCATA
CTTTTGTGGTTGACGTAGCTCAGGGGACCCAAATAACAGGAAGGAAAGCAGATGTTATTAAGGCAGCTCACCATTGTGCT
GAAGCTGCCCTATGCCTGGTCAAACCTGGAAATCAGAACACACAAGTGACAGAAACCGGGAACAAAGTTGCCCACTCATT
TAACTGCACGCCAACAGAAGGTATGCCTGTCACACCAGTTGAAGCAGCATGTCATCGATGGAGAAAAAAACCATTACTCA
GAATCCCACAGACCAGCAGAAGAAGGACCGTGAAAAAGCTGAATTTGAGGTACATGAAGTATATGCTGTGGATGTTCTCG
TCAGCTCAGGAGAGGGAAAGGCCAAGGATGCAGGACAGAGAACCACTATTTACAAACGAGACCCTTCCAAACAGTATGGA
CTGAAAATGAAAACCTGACGTGCCTTCTTTGGTGAGGTGGAAAGGCATTTTGATGCTACGCCGTTTACTTTCCGAGCATT
TGAAGATGAGAAGAAGGCTCAGATGGGTGTGGTGGAGCGCCCCAAGCATGGACTGCTGCGACCATTTAATGTTCTCTATG
AGAAGGAGGGGGAATTTGCTGCCCAGTTTAAATTTACAGTTCTGCTGATGCCCAGTGGCCCCATGCGGATAACCAGTGGT
CCCTTCCAGCCTGACCCCCATAAGTCTGAGATGGAGGTCCAGGATGCAGAGCTAAAGACCCTCCTCCAGGGTTCTGCAAG
T

Alignment

ORF - retro_mmul_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 74.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVGVAQGTQVTGRKA
          KK.IAFPTSISVNN.VCHFSPLKS.QDYILKEGDLVKIDLGVH.DGF.ANVAHTFVV.VAQGTQ.TGRKA
Retrocopy KKCIAFPTSISVNNGVCHFSPLKSGQDYILKEGDLVKIDLGVHADGFTANVAHTFVVDVAQGTQITGRKA

Parental  DVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGM-LSHQLKQHVIDGEK-TIIQNPTDQ
          DVIKAAH.CAEAAL.LVKPGNQNTQVTE..NKVAHSFNCTP.EGM.LSHQLKQHVIDGEK.TI.QNPTDQ
Retrocopy DVIKAAHHCAEAALCLVKPGNQNTQVTETGNKVAHSFNCTPTEGM>LSHQLKQHVIDGEK>TITQNPTDQ

Parental  QKKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPF
          QKKD.EKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKT.RAFF.EVER.FDA.PF
Retrocopy QKKDREKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKT*RAFFGEVERHFDATPF

Parental  TLRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEME
          T.RAFEDEKKA.MGVVE..KH.LL.PFNVLYEKEGEF.AQFKFTVLLMP.GPMRITSGPF.PD..KSEME
Retrocopy TFRAFEDEKKAQMGVVERPKHGLLRPFNVLYEKEGEFAAQFKFTVLLMPSGPMRITSGPFQPDPHKSEME

Parental  VQDAELKALLQSSAS
          VQDAELK.LLQ.SAS
Retrocopy VQDAELKTLLQGSAS

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	0.67 RPM	65.44 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	56.80 RPM
SRP007412_cerebellum	0.39 RPM	57.67 RPM
SRP007412_heart	0.18 RPM	59.95 RPM
SRP007412_kidney	1.17 RPM	54.22 RPM
SRP007412_liver	0.51 RPM	35.70 RPM
SRP007412_testis	0.08 RPM	155.18 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1168 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1168 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168 , retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,