RetrogeneDB ID: retro_mmul_2155

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:69600996..69601726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4299
• Ensembl ID: ENSMMUG00000022824
• Aliases: None
• Description: None

Sequence

>retro_mmul_2155
GTGGGCCTGGACCCAGGGCTGGTGCAGAAGTTTGGCTGCTTGGGCACCACCAACAAGGACGTGCTCATCTCTGAGTTCCA
GAGGCTGCTTGGCTTCCAGCTCAACTCTGCTGAGGGCACCTTCTTCCTGGACACGACCAGCTGGAACCTACAAGTAGCAA
TTGGTGCCTATTGTGACTCTGATAGCCCAAACATCAGTGTGCCCTCTATGTCCTTTGTTGAAGATGTCACCAAAGGAGAA
GCAGAGTCAATACCTCCTGATACTTAGTTTGTAAAATCATGGTAGATCCAGAATTCTGGGACAGAGGCCTGGCTTCCAGG
GGTTTGTCTTAAGTATGTCGGGGGAGACCAATTTGGACTTGTGAATGTGGTGATAGTGAGAGCACTAGAAGCCCCTCAAA
ATTGCAGATGTCAGCGTCCAGATGTGCAGCTCCAGCAGAGCAGGAATGTATCAGGGACAGTGGTGGATGTGCACTGCTAC
AGGACTCTGCTATGGAGCTGTTACCAGGAAGATTCTCCATGTAAAGGTGGGTGGACTTTTAGGAGTAATGCAGCCGCCGT
CATCTTTTGAAACTCAGCTCGATGCACCGCTGCATCCCAAGGTAGAAGGAAACTTCAATCAGCTTGCCTCTTCCCAAAAG
AACCAAGAATCAGATGAAAACAACTTAAAAGACCCTGGGGGTTCCGGGTTCCACCCAATCAGTGAAAACACACTGGCTCC
TGCTCCTGAC

Alignment

ORF - retro_mmul_2155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 81.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDLDPELMQKFSCLGTTDKDVLISEFQRLLGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNISVPSM
          V.LDP.L.QKF.CLGTT.KDVLISEFQRLLGFQLN.A...FFLD.T.WNLQ.AIGAY.D..SPNISVPSM
Retrocopy VGLDPGLVQKFGCLGTTNKDVLISEFQRLLGFQLNSAEGTFFLDTTSWNLQVAIGAYCDSDSPNISVPSM

Parental  SFVEDVTIGEGESIPPDTQFVKTWRIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLE-PQEIADVSV
          SFVEDVT.GE.ESIPPDT.FVK.W.IQNSG.EAW.PGVCLKYVGGDQFG.VN.V.VR.LE.P..IADVSV
Retrocopy SFVEDVTKGEAESIPPDT*FVKSW*IQNSGTEAWLPGVCLKYVGGDQFGLVNVVIVRALE>PLKIADVSV

Parental  QMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQLSSFETEFNTQPHRKVEGNFNPFA
          QMCS.SRAGMYQGQW.MCTATGL.YG.V...IL.V.VGGLLGV.Q..SSFET......H.KVEGNFN..A
Retrocopy QMCSSSRAGMYQGQWWMCTATGLCYGAVTRKILHVKVGGLLGVMQPPSSFETQLDAPLHPKVEGNFNQLA

Parental  SPQKNRQSDENNLKDPGGPEFDSISKNTWAPASD
          S.QKN..SDENNLKDPGG..F..IS.NT.APA.D
Retrocopy SSQKNQESDENNLKDPGGSGFHPISENTLAPAPD

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	136.70 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	229.58 RPM
SRP007412_cerebellum	0.00 RPM	242.35 RPM
SRP007412_heart	0.00 RPM	103.99 RPM
SRP007412_kidney	0.12 RPM	148.12 RPM
SRP007412_liver	0.00 RPM	172.55 RPM
SRP007412_testis	0.00 RPM	99.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2155 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2155 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155 ,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933, retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564,