RetrogeneDB ID: retro_mmul_2192

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:132206685..132207941(+)
• Located in intron of: ENSMMUG00000019346

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSMMUG00000021343
• Aliases: None
• Description: None

Sequence

>retro_mmul_2192
GGAATGGAGAGAATGGGGGTCCTTATTCTCTCATCTACTAGAGAACTAGCCATGCCAACTTTTGGTGTTCTTAAGGAGCT
AATGACTCACCACGTGCATACCTATGGGTTGATAATGGGTGGCAGTAACAGACCTGCTGAAGCATAGAAACTTGCTAATG
GGATCAACATCCTTGTGGTCACACCAGGCCATCTGCTGAACCATATGCAGAATATCCCAGGGTTTATGTATAAAAATCTG
AAGTGTCTGGTCGTCGATGAAGCTGATCGTATCTTGGATGTTGAGTTTGAAGAGGAATTAAAGCAAATTATTAAACTTTT
GCCAACACGTAGACAGACGATGCTTATTTCTGCCACCCAAACTCAAAAAGTTGAATGCCTGGCAAGGATTTCTCTGAAAA
AGGAGCCATTGTATGCTGGTGTTGATAACACAGCTAATGCAACAGTGGATGGTCTTGAGCAGGGATATGTTGTTTGTCCT
TCTGAAAAGAGATTCCTTCTGCTCTTTACATTCCTTAAGAAGAACCAAAAAAAATAAGCTGATGGCCTTCTTTTCATCTT
GTATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCCATCTTGGCCATTCATGGAAAGCAAAAGCAA
AATAAGCATACAACCACATTCTTCCAGTTCTGCAATGCAGATTCGGGAACACTATTGTGTACAGATGTGACAGCAAGAGG
ACTGGACATTACTGAAGTCGATTGGATTGTTCAGTATGACCCTCTGGATGACTCTAAGGAATAATATTCACCATGTGGGT
AGAACAGCCAGAGGCCTAAATGGGAGAGGGCATGCCTTGCTCATTTTGCACCCAGAAGAATTGGGTTTTCTTCACTACTT
GAAACAATCCAAGGTTCCGTCAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATTCAGTCTCAGCTTGAAAAGA
ACTACTTTCTTCACAAGTCAGCCCAGGAAACATAAAAATCATACATACAAGCCTATGATTCCCATTCTCTGAAACAGATC
TTTAATGTTAATAACTTCAATTTGCCTCAAGTTACTCTATCATTTGGTTTCAAGGTGCCTCCCTTTGCTGATCTGAATGT
CAACAGCAATGAAGGCGAGCAGAAAAAGCGAGTAGGCAGTGGTGGATTTGGCTACCAGAAAACCAAGAAAGTTGAGAAGT
CCAAAATCTTTAAACACATTAGCAAGAAAGTATCCAACAGTAGGCAGTTCTCTCAC

Alignment

ORF - retro_mmul_2192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.06 %
• Parental protein coverage: 63.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVGKMFTSVVAHRHHLVHVLALVPKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQ
          G...M..........L......V.KELMTHHVHTYGLIMGGSNR.AEA.KLANGINI.V.TPG.LL.HMQ
Retrocopy GMERMGVLILSSTRELAMPTFGVLKELMTHHVHTYGLIMGGSNRPAEA*KLANGINILVVTPGHLLNHMQ

Parental  NTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPSKK-TVLMPELYHSQVRYFADFS-EKEPLYVG
          N.PGFMYKNL.CLV.DEADRILDV.FEEELKQIIKLLP....T.L........V...A..S..KEPLY.G
Retrocopy NIPGFMYKNLKCLVVDEADRILDVEFEEELKQIIKLLPTRRQTMLISATQTQKVECLARISLKKEPLYAG

Parental  VDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKK-KLMVFFSSCMSVKYHYELLNYIDLPVLAIH
          VD...ANATVDGLEQGYVVCPSEKRFLLLFTFLKKN....KLM.FFSSCMSVKYHYELLNYIDLP.LAIH
Retrocopy VDNT-ANATVDGLEQGYVVCPSEKRFLLLFTFLKKNXXX>KLMAFFSSCMSVKYHYELLNYIDLPILAIH

Parental  GKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKE-YIHRVGRTARGLNGRGH
          GKQKQNK.TTTFFQFCNADSGTLLCTDV.ARGLDI.EVDWIVQYDP.DD.KE..IH.VGRTARGLNGRGH
Retrocopy GKQKQNKHTTTFFQFCNADSGTLLCTDVTARGLDITEVDWIVQYDPLDDSKE>NIHHVGRTARGLNGRGH

Parental  ALLILRPEELGFLRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSL
          ALLIL.PEELGFL.YLKQSKVP.SEFDFSWSKISDIQSQ.....EKNYFLHKSAQE..KSYI.AYDSHSL
Retrocopy ALLILHPEELGFLHYLKQSKVPSSEFDFSWSKISDIQSQ----LEKNYFLHKSAQET*KSYIQAYDSHSL

Parental  KQIFNVNNLNLPQVALSFGFKVPPFVDLNVNSNEGKQRKRGGGGGFGYQKTKKVEKSKIFKHISKKSSDS
          KQIFNVNN.NLPQV.LSFGFKVPPF.DLNVNSNEG.Q.KR.G.GGFGYQKTKKVEKSKIFKHISKK.S.S
Retrocopy KQIFNVNNFNLPQVTLSFGFKVPPFADLNVNSNEGEQKKRVGSGGFGYQKTKKVEKSKIFKHISKKVSNS

Parental  RQFCH
          RQF.H
Retrocopy RQFSH

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	0.56 RPM	26.33 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	21.82 RPM
SRP007412_cerebellum	1.10 RPM	45.14 RPM
SRP007412_heart	0.29 RPM	14.01 RPM
SRP007412_kidney	0.82 RPM	26.99 RPM
SRP007412_liver	0.16 RPM	10.61 RPM
SRP007412_testis	0.57 RPM	15.91 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2192 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2192 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1361
Pan troglodytes	retro_ptro_933
Pongo abelii	retro_pabe_1128

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116,
Choloepus hoffmanni	ENSCHOG00000004191	6 retrocopies	retro_chof_1221, retro_chof_1539, retro_chof_1636, retro_chof_2416, retro_chof_2418, retro_chof_721,
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297,
Homo sapiens	ENSG00000088205	6 retrocopies	retro_hsap_1361, retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192 ,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865,
Nomascus leucogenys	ENSNLEG00000011769	4 retrocopies	retro_nleu_1377, retro_nleu_1396, retro_nleu_266, retro_nleu_437,
Ochotona princeps	ENSOPRG00000001701	1 retrocopy	retro_opri_1039,
Pongo abelii	ENSPPYG00000012796	4 retrocopies	retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes	ENSPTRG00000012391	5 retrocopies	retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,