RetrogeneDB ID: retro_mmul_1991

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:174019845..174020324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSMMUG00000003248
• Aliases: None
• Description: cyclin-H [Source:RefSeq peptide;Acc:NP_001253375]

Sequence

>retro_mmul_1991
CCTATAGACCACTGGAGTGCTTCCTCACAGACTTACTATGCAATGCTGGAGAATCCAGACATTTTGAGGAAAACAGTTGA
TGAACTTCTTAATAGAATCACATTGACGGCTGCTTACCATTTATACACACCTTCCCAAATTGCCCTGCCTGCCATTTTAT
CTAGTGCCTTCAGGGCTGGAATTACTATGGAAAGTTAGTTGTTTATTGGACAGTCTGGTTTTGAGAGAGAACAGAACTTG
CTTGTCACAGTTACTAGATATAATGAAAAGCAGGAGAAATTGAGTAAAAAAGTATGTACCACCCAGATCTGAAGAAACTG
CTGTTCTGAAGCCGAAGTTGGAGCAATGTCATTCTGCTGAGCTTGCACTTAATGTAATTGCGAAGAAAAGGAAAGGCTGT
GGAAGATAATGATGATGTCTCAAAGAAATACAGACAGGAGGAGGAAGAGTAGACTGATGATGACCTGGTAGACTCTCTC

Alignment

ORF - retro_mmul_1991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.35 %
• Parental protein coverage: 58.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PFEGFLIDLKTRYPMLENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMES--YLS
          P.........T.Y.MLENP.ILRKT.D..LNRI.LT.AY.LYTPSQIAL.AILSSA.RAGITMES.....
Retrocopy PIDHWSASSQTYYAMLENPDILRKTVDELLNRITLTAAYHLYTPSQIALPAILSSAFRAGITMES*LFIG

Parental  ESLMLRENRTCLSQLLDIMKSMRNLVKK-YEPPRSEEVAVLKQKLERCHSAELALNVITKKRKG-YEDDD
          .S...RE....L............L.KK.Y.PPRSEE.AVLK.KLE.CHSAELALNVI.KKRKG..ED.D
Retrocopy QSGFERE-QNLLVTVTRYNEKQEKLSKK>YVPPRSEETAVLKPKLEQCHSAELALNVIAKKRKG>VEDND

Parental  YVSKKSKHEEEEWTDDDLVESL
          .VSKK...EEEE.TDDDLV.SL
Retrocopy DVSKKYRQEEEE*TDDDLVDSL

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	35.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.83 RPM
SRP007412_cerebellum	0.00 RPM	41.78 RPM
SRP007412_heart	0.00 RPM	13.43 RPM
SRP007412_kidney	0.00 RPM	19.48 RPM
SRP007412_liver	0.00 RPM	10.05 RPM
SRP007412_testis	0.00 RPM	52.96 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1991 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1991 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1991 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3128
Pan troglodytes	retro_ptro_2116
Gorilla gorilla	retro_ggor_2143
Pongo abelii	retro_pabe_2584

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991 ,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,