RetrogeneDB ID: retro_mmus_2366

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:76837744..76838815(+)
• Located in intron of: ENSMUSG00000028399

Retrocopy information

• Ensembl ID: ENSMUSG00000084090
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Drg1
• Ensembl ID: ENSMUSG00000020457
• Aliases: Drg1, AA408859, AI132520, Nedd3
• Description: developmentally regulated GTP binding protein 1 [Source:MGI Symbol;Acc:MGI:1343297]

Sequence

>retro_mmus_2366
ATCAGCGGGACCTCAGGGAAGACCCCTGGAAGTGAAGCTGAGATGTCACAGACTCAGAAGAACAAATTTACAACACATCA
TCTTGGGTTCTTTAAGGTTTGCCTTGCCAAGGTTGAAGAGAACTCCATAAAGTGGGCATAGTGGTAGACCAGGAGAAGGT
TGTGATAGGGACACCACAGGCATTGATCAAATTGGATTTGTGGGTTTCCATATGTGGGGAAGTCAACTCTGCTAAATAAC
CTAGCAGGAGTGAATTTTCAACTGGCAGCCTAGGAATTCACTGCTTTGACCACTGTGTATGATGTCATCAGATATAAACG
TGCCTGGATTGTTCAGGTATTATTGATGATGTCATTGAGGGAAAGGGCAGAGGTCACCAAGCCATTGTAGTGGGTTGAGC
ATGTAATTTGATCTTGATTATTCTGGCTGTCCTAAAACCCATGGCATGTAAGATAACTGAAAATGAGTTGGAAAGCTTTG
GGATTCGCTTGAACAGCAAACCTCCCAACATTGGCTTTAAGAAGAAAGACAAAGGAGGCATTAATCTCACAGCCACATGC
CCTCAGAGTGAACTAGATGCTTGAAACAGCAAAGAACATTTTGGCTGAATACAAAAATCATAATGCTGACATGAGTTTAC
ATAATGATACTGTAGCCAAATGACCCCGTTGACGTGGCAGAAGGAAACAGAGTTCATAGTTCCTGTGCCTATGTACTAAA
TATGATTGTTCAGGTCTCCACTGAGGAATTGGATATTATCTATAAGGTGCCTCACTGCAAACACATTTCTGCCTATCACC
ACTGGGGCTTTGATGGTCTGTTGGAGAGGATCGGGAACTATTTCAAACTAGTAAAAATTTACACTAATCTCAAGGGCCAG
TTACCAGACAGTTGGTCAACAGTGGTGCTACCTTACTCTCAAATCATGGTGGGATATTTCTGCATGAAGATTCACAAAAA
TCTTAGCAAAAACTTAAATATATTTTGGTCTGAGATCTCTCAGTGAAATGCAATTCTTAGACTGCAGATAAAGAACATAC
ATTGAAAGATGTCCTTCTGATGGTGAAAAAG

Alignment

ORF - retro_mmus_2366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSGTLAKIAEIEAEMARTQKNKATAHHLGLLKARLA-KLRRELITPKGGGGGGPGEGFDVAKTGDARIGF
          .SGT..K....EAEM..TQKNK.T.HHLG..K..LA..L.R...TP..G..G.PGEG.D...TG...IGF
Retrocopy ISGTSGKTPGSEAEMSQTQKNKFTTHHLGFFKVCLA>RLKR---TP*SGHSGRPGEGCDRDTTGIDQIGF

Parental  VGF-PSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGVIRYKGAKIQLLDL-PGIIEGAKDGKGRGRQVIA
          VGF.P.VGKSTLL.NLAGV....AA.EFT.LTTV..VIRYK.A.I....L....IEG...G.G...Q.I.
Retrocopy VGF<PYVGKSTLLNNLAGVNFQLAA*EFTALTTVYDVIRYKRAWIVQVLL<DDVIEG--KGRG--HQAIV

Parental  VARTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDA-ETVK
          V...CNLILI.L.VLKP....KI.ENELE.FGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDA.ET.K
Retrocopy VG*ACNLILIILAVLKPMA-CKITENELESFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDA>ETAK

Parental  SILAEYKIHNADVTLRSDATA-DDLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHR
          .ILAEYK.HNAD..L..D..A..D..DV.EGNRV...C.YVLN.I.Q.S.EELDIIYKVPHC..ISA.H.
Retrocopy NILAEYKNHNADMSLHNDTVA>NDPVDVAEGNRVHSSCAYVLNMIVQVSTEELDIIYKVPHCKHISAYHH

Parental  WNFDDLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIK-EFKYALVWGLSVK
          W.FD.LLE.I..Y.KLV.IYT..KGQLPD..S.VVLPYS...V..FCMKIHKNL.K...KY.LV..LSVK
Retrocopy WGFDGLLERIGNYFKLVKIYTNLKGQLPDSWSTVVLPYSQIMVGYFCMKIHKNLSK<KLKYILV*DLSVK

Parental  HNPQKVGKDHTLEDEDVIQIVKK
          .N.....K.HTL...DV...VKK
Retrocopy CNS*TADKEHTL--KDVLLMVKK

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	0.07 RPM	50.81 RPM
SRP007412_cerebellum	0.04 RPM	40.08 RPM
SRP007412_heart	0.00 RPM	26.83 RPM
SRP007412_kidney	0.00 RPM	37.54 RPM
SRP007412_liver	0.00 RPM	29.30 RPM
SRP007412_testis	0.00 RPM	91.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2366 was not detected

EST

No EST(s) were mapped for retro_mmus_2366 retrocopy.

TSS

No TSS is located nearby retro_mmus_2366 retrocopy 5' end.

Lab

retro_mmus_2366 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2366 has 0 orthologous retrocopies within eutheria group .

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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	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366 ,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,