RetrogeneDB ID: retro_mmul_2208

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:16773286..16773758(-)
• Located in intron of: ENSMMUG00000018332

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12033
• Ensembl ID: ENSMMUG00000005321
• Aliases: None
• Description: carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 [Source:RefSeq peptide;Acc:NP_001252987]

Sequence

>retro_mmul_2208
TTTAAGCCCAGCAACAATGCTAGCTTCACAGTGCCTACAGAGATTGAGGAGACCACTCAAGCAGGTATATGTGCTCAAGA
GGCCTCGCGCAAAAAGACAAATGAGAGAACTCTTTGAATGTGTTCTCTTCACTGCCAACCTGGCCAAGTATGCTGACCTG
TGACAGATCTGCTGGACCAGTGTGGGTGTTCCGAGCTCACCTATTCCATGAGTCCTGTGGTTCCACCAGGGCTGCTAAGT
CAGGAACCTCAGCCTCCTGGGGAGGAACCTGAGGAAAACCCTCATCCTGGACAACCTGTCTGCTTCTTACATCTTCCACC
CAGAGAATGCAGTGTCTGTGCAGTCCTGGTTTGATGACATGGCAGATACTGAGTTGCTGAACCTGATCCCAGTCTTTGAG
GAGCAGAGCAGAGGACGTCTACACCAGCCTCGGGTAGGTGCAGGCCTCTTAGCCTTCCCTGCTTCCAAGCAG

Alignment

ORF - retro_mmul_2208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.89 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FKPINNADFIVPIEIEGTTH-QVYVLKRPYVDEFLRRMGELFECVLFTASLAKYAD-PVTDLLDRCG-VF
          FKP.NNA.F.VP.EIE.TT..QVYVLKRP......R.M.ELFECVLFTA.LAKYAD.PVTDLLD.CG.VF
Retrocopy FKPSNNASFTVPTEIEETTQ>QVYVLKRPRAK---RQMRELFECVLFTANLAKYAD<PVTDLLDQCG<VF

Parental  RARLFRESCV-FHQGCYVKDLSRLGRDLRKTLILDNSPASYIFHPENAVPVQSWFDDMADTELLNLIPIF
          RA.LF.ESC..FHQGC.V..LS.LGR.LRKTLILDN..ASYIFHPENAV.VQSWFDDMADTELLNLIP.F
Retrocopy RAHLFHESCG<FHQGC*VRNLSLLGRNLRKTLILDNLSASYIFHPENAVSVQSWFDDMADTELLNLIPVF

Parental  EELSGAEDVYTSLGAAGPLACPASKQ
          EE.S.........G.AG.LA.PASKQ
Retrocopy EEQSRGRLHQPRVG-AGLLAFPASKQ

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	95.69 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	120.90 RPM
SRP007412_cerebellum	0.26 RPM	154.79 RPM
SRP007412_heart	0.00 RPM	125.90 RPM
SRP007412_kidney	0.23 RPM	189.67 RPM
SRP007412_liver	0.08 RPM	132.01 RPM
SRP007412_testis	0.00 RPM	125.10 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2208 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2208 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Homo sapiens	ENSG00000175215	2 retrocopies	retro_hsap_4315, retro_hsap_4319,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208 , retro_mmul_764,
Macaca mulatta	ENSMMUG00000016742	1 retrocopy	retro_mmul_2621,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612,
Nomascus leucogenys	ENSNLEG00000017164	2 retrocopies	retro_nleu_1741, retro_nleu_3079,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20, retro_pmar_27,
Pongo abelii	ENSPPYG00000004711	14 retrocopies	retro_pabe_1708, retro_pabe_1739, retro_pabe_1740, retro_pabe_1742, retro_pabe_1746, retro_pabe_1762, retro_pabe_2402, retro_pabe_2592, retro_pabe_3202, retro_pabe_3205, retro_pabe_3221, retro_pabe_3237, retro_pabe_3554, retro_pabe_3578,
Pan troglodytes	ENSPTRG00000005155	7 retrocopies	retro_ptro_2587, retro_ptro_2589, retro_ptro_2590, retro_ptro_2592, retro_ptro_2594, retro_ptro_2958, retro_ptro_3054,