RetrogeneDB ID: retro_mmul_2240

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:83228737..83229425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSMMUG00000017908
• Aliases: None
• Description: None

Sequence

>retro_mmul_2240
ATGAAAGACCAGCATTTATGAGGTTCCTTCTCAGAGTCCACATCATTCAATATTTTGATGGATATGTTAGTTGTCAAAGG
CAGATATAAAAGTGCTTTGGAAGTATTGATAGAGATGAAAAATCAAAGTGTGAAATTCACCAAAGATACCTATGTTCTTA
CTTTTGCAGTTTGCTACAAACTGAATAGCCCTGAGTCTTTCAAAATCTGTTCTACATTAAGAGAAGAAGCCCTACTCAAA
GGACAGGTTCTCTCCAGGAAAGCATCCCATTTCTTTGTGGTGTGAACTCTGAATCAGAACCAGGTGGCAAAAGCTATGTC
CATTTTTTTCTCAAATCATGAATCCAGAAAGCATAGCCTGCACTAATTTAACTATTATAATCTATATCCAGTCAAATAAT
GTTGGAAACCCTGATAGAGATACTAAAAAATGCTGCAGAAGGAAATTTATTAAAATTTGTTAAAAGACATGAATTCTCAG
AGGAAGTGCTGGCCAAAGTGAAGGAAAAGTGAAGGATGTGCCTGCCCTTGTGGCCAGATTTAATGAGATCTATGGGAAAC
TGCACATCAGTGGCCAGGTCACCACTTGTACTTTGGGTGCTCTGCTCTGCCACACTCCCAGGGACAGGAAATACCATATG
TTGCTATTAAACAAGAGGATGATGACCCATCGGACCTTCCAATCACTC

Alignment

ORF - retro_mmul_2240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTDDHLRGFFSDSTSFNILMDMLFIKGKYESALEVLIEMKNQDVKFTKDTYVLAFAICYKLHCGHSSEVC
          M.D.HL.G.FS.STSFNILMDML..KG.Y.SALEVLIEMKNQ.VKFTKDTYVL.FA.CYKL....S...C
Retrocopy MKDQHL*GSFSESTSFNILMDMLVVKGRYKSALEVLIEMKNQSVKFTKDTYVLTFAVCYKLNSPESFKIC

Parental  FPSGANVLILNVFIFRKLKLAISDSFMGKNELAKAVSI-FSQIMNPESIACTNLNVIIHIQSN-ALENLI
          .......L.......RK............N..AKA.SI.FSQIMNPESIACTNL..II.IQSN..LE.LI
Retrocopy STLREEALLKGQVLSRKASHFFVV*TLNQNQVAKAMSI>FSQIMNPESIACTNLTIIIYIQSN>MLETLI

Parental  ETLTNAAEGNLSKFVKRHMFSEEVLAKVRE-KVKDVPALVAKFDEIYGKLHISGQVTNYSLDAVLCYTPR
          E.L.NAAEGNL.KFVKRH.FSEEVLAKV.E.KVKDVPALVA.F.EIYGKLHISGQVT...L.A.LC.TPR
Retrocopy EILKNAAEGNLLKFVKRHEFSEEVLAKVKE<KVKDVPALVARFNEIYGKLHISGQVTTCTLGALLCHTPR

Parental  DKKSHTLLLNKRMVIRRTFRPL
          D.K.H.LLLNKRM...RTF..L
Retrocopy DRKYHMLLLNKRMMTHRTFQSL

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	0.78 RPM	11.88 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.36 RPM
SRP007412_cerebellum	0.58 RPM	7.36 RPM
SRP007412_heart	0.35 RPM	15.02 RPM
SRP007412_kidney	0.35 RPM	12.68 RPM
SRP007412_liver	0.16 RPM	7.09 RPM
SRP007412_testis	0.23 RPM	4.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2240 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2240 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240 ,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,