RetrogeneDB ID: retro_mmul_1137

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:22276219..22277154(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009812
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSMMUG00000019916
• Aliases: None
• Description: None

Sequence

>retro_mmul_1137
GGGCGGGCTGCCGGCGTGGCTGGGCGCGGTCAAGCTGCGGATCAGGCCCTGGCCTGCGCGCTGTGCAGCCGCCTGCTCTC
CTTCCTGCTACAGATGTACGCGCTGCTGTGTGCCGCGCCGACGCCTTCCACCGTGGCATCTTCCTCTTCCACTGCCGTGA
GCCGCCGTGCTGTGCCGGCCTGCGAGTTTTTAGGAATCAGCTACCCAGGAAAAATGATTTTTACTCATATGAGCCACCTT
CTGAGAATCCTTCCCCAGAAACAGGACAATCAGTGTGTCTCCAACTTAAGTCTAGTGCTGGTCTCTGCAGAGTTTGTGGC
TGTTTAGGCCCCAAAACATGCTCCAGATGCCACAAAGCGTATTACTGCAGCAAGGAGCATCAGAGCCTAGACCAGAAATT
GACATATAAACAGGCTTGTACACAATCAGATCATTTGGACCACATAATTCCAGACCACGACTTCCTTTTTCCAGAATTTG
CAATTGTAATAGAAGCAAAAGATGAGATTACACCTGAAGTTGTGGAAAAGGAAGATTACTCGGAGATTATAGGGAGCATG
GGTGATGCACTTGACGAAGAACTGGATTCCATGGCAAAACATGAATCCAGGGAAGATAACATTTTTCAGAAGTTCAAAAC
TCAGATAGCCTTTGAACCGGAACAGATTCTCAGATATGGCAGAGGTATTGCCCCCATCTGGATTTCAGGTGAAAATATTC
CTCAAGAAAAGGATATTCCAGAGAATATCCTTTGTGATGCCAAGAGAATGTTTGAATTCCAGGTTATGCCTCAGCTCCTA
AACTACCTGAAGGCTGGCAGACTGGGCAAGAGCATTGACTGGGGCATCCTGGATATCTTCACCTGGGCTGAGAGCTGCAG
CTTGGGTACTGGCTCTACAGAATAATTTGTGTGGAAGCAGGATGTAACAGATACA

Alignment

ORF - retro_mmul_1137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.79 %
• Parental protein coverage: 90.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRPAWLGAAGLPGPRALACALCGRPLSFLLQVYAPLPG-RADAFHRGIFLFCCREPPCCAGLRVFRNQLP
          GR.A.....G.....ALACALC.R.LSFLLQ.YA.L...RADAFHRGIFLF.CREPPCCAGLRVFRNQLP
Retrocopy GRAAGVAGRGQAADQALACALCSRLLSFLLQMYALLCA<RADAFHRGIFLFHCREPPCCAGLRVFRNQLP

Parental  RKNDFYSYEPPSENPPPETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQTLDWRLGHKQT
          RKNDFYSYEPPSENP.PETG.SVCLQLKS.A.LCRVCGCLGPKTCSRCHKAYYCSKEHQ.LD..L..KQ.
Retrocopy RKNDFYSYEPPSENPSPETGQSVCLQLKSSAGLCRVCGCLGPKTCSRCHKAYYCSKEHQSLDQKLTYKQA

Parental  CAQPDHFDHIIPDHNFLFPEFEIVIETEEEIMPEVVEKEDYSEITGSMGEALEEELDSMAKHESREDTIF
          C.Q.DH.DHIIPDH.FLFPEF.IVIE...EI.PEVVEKEDYSEI.GSMG.AL.EELDSMAKHESRED.IF
Retrocopy CTQSDHLDHIIPDHDFLFPEFAIVIEAKDEITPEVVEKEDYSEIIGSMGDALDEELDSMAKHESREDNIF

Parental  QKFKTQIALEPEQILRYGRGIAPIWISGENIPQEKDIPD-CPCGAKRILEFQVMPQLLNYLKADRLGKSI
          QKFKTQIA.EPEQILRYGRGIAPIWISGENIPQEKDIP....C.AKR..EFQVMPQLLNYLKA.RLGKSI
Retrocopy QKFKTQIAFEPEQILRYGRGIAPIWISGENIPQEKDIPENILCDAKRMFEFQVMPQLLNYLKAGRLGKSI

Parental  DWGILAVFTCAESCSLGTGYTEEFVWKQDVTAT
          DWGIL..FT.AESCSLGTG.TE.FVWKQDVT.T
Retrocopy DWGILDIFTWAESCSLGTGSTE*FVWKQDVTDT

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	16.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.30 RPM
SRP007412_cerebellum	0.00 RPM	15.69 RPM
SRP007412_heart	0.00 RPM	10.36 RPM
SRP007412_kidney	0.00 RPM	16.67 RPM
SRP007412_liver	0.00 RPM	12.90 RPM
SRP007412_testis	0.00 RPM	1.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1137 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1137 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2915

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Cavia porcellus	ENSCPOG00000002920	1 retrocopy	retro_cpor_168,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137 ,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,
Ictidomys tridecemlineatus	ENSSTOG00000022768	2 retrocopies	retro_itri_1348, retro_itri_1635,