RetrogeneDB ID: retro_mmus_2648

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:41853608..41854201(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tpgs2
• Ensembl ID: ENSMUSG00000024269
• Aliases: Tpgs2, 5730437P09Rik, 5730494M16Rik, AI666318, Pgs2
• Description: tubulin polyglutamylase complex subunit 2 [Source:MGI Symbol;Acc:MGI:1913898]

Sequence

>retro_mmus_2648
ATGGAGGAGACACCAACCCCACTGCAAGCCAGCAGCAAGCCGCACCTTGAGAAGTGGACCCTGGGCGTCACTCGCCTCCT
GGAAACTTCCCCAGGTGTGACAGGGGTGAGCATAATAGAAAAGCTGCCTGCTGAACATCATATGATTTCTTCCTGGGAAC
AGAAAAACAATTGTGCGATGCCTGAGGATGTGAGAAACTTCTACTTGATGACCAGTGGTTTCCACATGACCTGGAGTGTG
AAGCTAAACGACCACATGATTCCACGGGGATGCATGGTGACTAACGGCATTTCAAAACTGACTTGGCTCATCCACTCTTC
TGTGTACTCACTTCCTAATGCGCCAACTCTGGCAGACTTAGAGGAGATACTCAAGAAGGAAATGAAGCCCACCCTCTAGG
GAAGCCTCACTTTGACTGTCGCAGTGCAATATTTGAGCTGGATTCATGCAATGGGAATGGGAAAGTTTGCCTCGTCTACA
AAAATGGGAAACCTGGATTAGCTCATGACACTGAGATATGGTTCCTGGACAGAGCATTATACTGGCACTTCCTCACAGAT
ATGCTTACTGCCTATTACCGCCTGCTCATCACA

Alignment

ORF - retro_mmus_2648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 66.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEETTPPLQAGSKPHLEKLTLGVTRILESSPGVTEVSIIEKLPAERHMISSWEQKNNCVMPEDVRNFYLM
          MEET..PLQA.SKPHLEK.TLGVTR.LE.SPGVT.VSIIEKLPAE.HMISSWEQKNNC.MPEDVRNFYLM
Retrocopy MEETPTPLQASSKPHLEKWTLGVTRLLETSPGVTGVSIIEKLPAEHHMISSWEQKNNCAMPEDVRNFYLM

Parental  TNGFHMTWSVKLDEHIIPLGSMVINGISKLTQLIQSSVYSLPNAPTLADLED-DTQEGNEDHQLEKPHFD
          T.GFHMTWSVKL..H.IP.G.MV.NGISKLT.LI.SSVYSLPNAPTLADLE..DTQEGNE.H.L.KPHFD
Retrocopy TSGFHMTWSVKLNDHMIPRGCMVTNGISKLTWLIHSSVYSLPNAPTLADLEE<DTQEGNEAHPLGKPHFD

Parental  CRSAIFELDSCNGNGKVCLVYKNGKPGLAHDTEIWFLDRALYWHFLTDTFTAYYRLLIT
          CRSAIFELDSCNGNGKVCLVYKNGKPGLAHDTEIWFLDRALYWHFLTD..TAYYRLLIT
Retrocopy CRSAIFELDSCNGNGKVCLVYKNGKPGLAHDTEIWFLDRALYWHFLTDMLTAYYRLLIT

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	0.02 RPM	46.87 RPM
SRP007412_cerebellum	0.04 RPM	28.27 RPM
SRP007412_heart	0.03 RPM	9.34 RPM
SRP007412_kidney	0.08 RPM	9.74 RPM
SRP007412_liver	0.00 RPM	4.83 RPM
SRP007412_testis	0.23 RPM	178.75 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2648 was not detected

EST

No EST(s) were mapped for retro_mmus_2648 retrocopy.

TSS

No TSS is located nearby retro_mmus_2648 retrocopy 5' end.

Lab

retro_mmus_2648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017766	3 retrocopies	retro_cfam_355, retro_cfam_457, retro_cfam_626,
Choloepus hoffmanni	ENSCHOG00000007960	1 retrocopy	retro_chof_1642,
Erinaceus europaeus	ENSEEUG00000005257	3 retrocopies	retro_eeur_208, retro_eeur_324, retro_eeur_516,
Myotis lucifugus	ENSMLUG00000001739	1 retrocopy	retro_mluc_1194,
Mustela putorius furo	ENSMPUG00000001097	2 retrocopies	retro_mputfur_1622, retro_mputfur_507,
Mus musculus	ENSMUSG00000024269	1 retrocopy	retro_mmus_2648 ,
Otolemur garnettii	ENSOGAG00000008218	1 retrocopy	retro_ogar_686,
Rattus norvegicus	ENSRNOG00000014957	1 retrocopy	retro_rnor_2961,
Sus scrofa	ENSSSCG00000026953	1 retrocopy	retro_sscr_590,
Tarsius syrichta	ENSTSYG00000005299	2 retrocopies	retro_tsyr_1161, retro_tsyr_512,
Tursiops truncatus	ENSTTRG00000007153	1 retrocopy	retro_ttru_1112,