RetrogeneDB ID: retro_mmul_1616

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:80501834..80502583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC4
• Ensembl ID: ENSMMUG00000006754
• Aliases: None
• Description: tetratricopeptide repeat protein 4 [Source:RefSeq peptide;Acc:NP_001253091]

Sequence

>retro_mmul_1616
GTGGAGCAACATGAGCAGGACCCCACCTCAGACGACACCATGAACTCGTTCCTGGAAAAGTTCCAGAGCCAGCCTTACCG
TGGCGGCTTTCATGAGGAACAGTGGGAGGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGTGCCATCAGAAATTG
ATCCCAGGGAGAATCCTGACTTGGCTTGTCTCCAGTCAATTATTTCTGATGAGGAGCTTTCTCCAGAAGAACAGGCCAAT
ACCTATAAAGATGAGGGCAATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTGATTTCCTACACTGAAGGATTAAA
GAAGAAATGTGCAAATCCTGATTTGAATGCTGTCCTTTATACCAACCGGGCAGCAGCACAGTACTATCTGGGCAATTTTC
GTTCTGCTGTCAGTAATTTGACAGCTGCCAGAAAGCTAAAATCCTGCTACCTCAAAGCAATAAGAGGTGCTTATGCCATC
TGGAACTGAAATACTTTGCCAAGGCTGTGAACTGATGTGATAAGGGACTGCAGATAGATGCCAAAGTGAAGAAGCTTCTG
GAAATGAGGGCTAAAGCAGACAAGCTGAAGCAAATTGAACAGAGGGATGTGGGGAAATCCAACTTGAAAGAAAAGGAGAG
GAATCAGAATGAGGCTTTACTCGAGGCCGTCAAGGCTAGGAATATCAGGTTCTCTGAAACTACCTGTGAGGATGAAATTT
CAGCCTCAGAAGATCTAGGGGACCTTTTT

Alignment

ORF - retro_mmul_1616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEQPGQNPTSDDVMDSFLEKFQSQPYRGGFHEDQWEEEFEKVPLFMKRAPSEIDPRENPDLACLQSIIFD
          .EQ..Q.PTSDD.M.SFLEKFQSQPYRGGFHE.QWEEEFEKVPLFMK..PSEIDPRENPDLACLQSII.D
Retrocopy VEQHEQDPTSDDTMNSFLEKFQSQPYRGGFHEEQWEEEFEKVPLFMKKVPSEIDPRENPDLACLQSIISD

Parental  EERSPEEQAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGNFRSALNDV
          EE.SPEEQA.TYKDEGNDYFKEKDYKKAVISYTEGLKKKCA.PDLNAVLYTNRAAAQYYLGNFRSA....
Retrocopy EELSPEEQANTYKDEGNDYFKEKDYKKAVISYTEGLKKKCANPDLNAVLYTNRAAAQYYLGNFRSAVSNL

Parental  TAARKLKPCHLKAIIRGA-LCHLELKHFAEAVNWCDEGLQIDGKEKKLLELRAKADKLKRIEQRDVRKAS
          TAARKLK.C.LKA.IRGA.LCHLELK.FA.AVN.CD.GLQID.K.KKLLE.RAKADKLK.IEQRDV.K..
Retrocopy TAARKLKSCYLKA-IRGA<LCHLELKYFAKAVN*CDKGLQIDAKVKKLLEMRAKADKLKQIEQRDVGKSN

Parental  LKEKKERNQNEALLQAIKARNIRLSEAACEDEDSPSEGLGELF
          LKE.KERNQNEALL.A.KARNIR.SE..CEDE.S.SE.LG.LF
Retrocopy LKE-KERNQNEALLEAVKARNIRFSETTCEDEISASEDLGDLF

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	13.56 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.23 RPM
SRP007412_cerebellum	0.00 RPM	11.56 RPM
SRP007412_heart	0.00 RPM	6.83 RPM
SRP007412_kidney	0.00 RPM	10.45 RPM
SRP007412_liver	0.00 RPM	5.38 RPM
SRP007412_testis	0.11 RPM	10.18 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1616 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1616 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3843
Pan troglodytes	retro_ptro_2620
Gorilla gorilla	retro_ggor_2588

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000005420	1 retrocopy	retro_ggor_2588,
Macaca mulatta	ENSMMUG00000006754	1 retrocopy	retro_mmul_1616 ,
Nomascus leucogenys	ENSNLEG00000003044	1 retrocopy	retro_nleu_1978,