RetrogeneDB ID: retro_mmus_2310

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:140116624..140117830(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dgcr14
• Ensembl ID: ENSMUSG00000003527
• Aliases: Dgcr14, AI462402, D16H22S1269E, Dgcr1, Dgsi, ES2, Es2el
• Description: DiGeorge syndrome critical region gene 14 [Source:MGI Symbol;Acc:MGI:107854]

Sequence

>retro_mmus_2310
GCTGAGGAAAATGGAGATTTGGAGCGCATGTGCCAGATTGCCATCAAGTTTGACTCTGCCCTGGACAAGATATCTCGGAA
ACCTACACCACCCTATGTTACTCCAGCCACCTTTGAAACTCCTGAGGTATACCTGGGCTCTGGTGTGCTGGGTAGCAAGC
CCCAGCCCCAGGGCCGAGACCTAGATGACAGATCAGCTGGAGATGAGAAGCAGGAGCCACTGCCCACCCTGGATGTCTAC
TTGAGCCACTACACAAGCGAGGACAACGCCGTATTCCAGAAGATCATGGAAGTGGCTAAGGGAAAAAGCCATGCCCACCA
TATTTGGCTCTACCAGGCTGAGGAGGAATTTGAGAAGCGACAGAAAGATAATCTTGAAAACCCATCAGCAGAAACTAAGC
CATTGAGAATAGTCGGGCTGGAGTGGAATCCTGGAAGTACAAGGCCAAGAATTCTCTCATGTACTATCCCAAGGGTGTGC
CTGATATCAAACAGTTGTTCAAGGAGCCGCTTCAGGTAGTACATAAGAACACACGTTTCCTCCAGGACCCCTTCAGTCAG
GTTCTGAGCAAATCCCAGCTTCAGCAAGCAGCTGCCCTCAATGCTCAGCACAAACTGGGCAATGTTGGCCCAGATGGCAA
GGAACTCATTCCCCAGGAGTCCCCCAGAGTGAATGGCTTTGGATTCGTTGCCACTCCTTCCCCTGCTCCTGGTATGAATG
AGTCCCCACTGATGGTGTGGGGACAGGTTGAGAACACACCCCTGCTAATCGAAGGGTCCGAGAGCCCCTATGTGGACAGG
ACACTGGGACCCGTGTTCAAGATCTCAGAGCCAGGACCCAGGGAGCGTCTGGGACTGAAGATAGCCAATGAAGCAGCTGC
CAAAAACCGGGCCATGAAGCATAAAGCATTGCAGAGAGTTACAGGGAACTTGACCAGTCTTACTCGCAAAGGCCTGAGCC
CAGCCATGTCCCCAGCCCTACATCGCCCCGTAAGCAGGACAGCAAGCAGGTATACAGATCTTGCCCTGTGGGCCAGCCAT
ACACCATCCCCAGCATGCTCTACCCACCTCAAGAACCCAACTGCTGGGCCGCAGACACCCACAAGCATCCCAGCCCTAAC
AGGTACACCCCTCACACAGGATCCAGCCTCTATCACAGACAACCTGCTGCAGTTTCCCCGCCCGGCACAAAGCTTCAGAC
TTCTTT

Alignment

ORF - retro_mmus_2310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.2 %
• Parental protein coverage: 84.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEENGDLERMRQIAIKFGSALGKISREPPPPYVTPATFETPEVHPGSAVLGNKPRPQGRDLDDAGEAGEE
          AEENGDLERM.QIAIKF.SAL.KISR.P.PPYVTPATFETPEV..GS.VLG.KP.PQGRDLDD...AG.E
Retrocopy AEENGDLERMCQIAIKFDSALDKISRKPTPPYVTPATFETPEVYLGSGVLGSKPQPQGRDLDDRS-AGDE

Parental  EEKEPLPSLDVFLSQYTSEDNASFQEIMEVAKEKSHARHAWLYQAEEEFEKRQKDNLELPSAEHQ-AIES
          ...EPLP.LDV.LS.YTSEDNA.FQ.IMEVAK.KSHA.H.WLYQAEEEFEKRQKDNLE.PSAE...AIE.
Retrocopy KQ-EPLPTLDVYLSHYTSEDNAVFQKIMEVAKGKSHAHHIWLYQAEEEFEKRQKDNLENPSAETK<AIEN

Parental  SQAGVETWKYKAKNSLMYYPEGVPDEEQLFKKPRQIVHKNTRFLRDPFSQALSRSQLQQAAALNAQHKQG
          S.AGVE.WKYKAKNSLMYYP.GVPD..QLFK.P.Q.VHKNTRFL.DPFSQ.LS.SQLQQAAALNAQHK.G
Retrocopy SRAGVESWKYKAKNSLMYYPKGVPDIKQLFKEPLQVVHKNTRFLQDPFSQVLSKSQLQQAAALNAQHKLG

Parental  KVGPDGKELIPQESPRVGGFGFVATPSPAPGVNESPLMTWGEVENTPLRVEGSESPYVDRTPGPTFKILE
          .VGPDGKELIPQESPRV.GFGFVATPSPAPG.NESPLM.WG.VENTPL..EGSESPYVDRT.GP.FKI.E
Retrocopy NVGPDGKELIPQESPRVNGFGFVATPSPAPGMNESPLMVWGQVENTPLLIEGSESPYVDRTLGPVFKISE

Parental  PGRRERLGLKMANEAAAKNRAKKQEALRRVTENLASLTPKGLSPAMSPALQRLVSRTASKYTDRALRASY
          PG.RERLGLK.ANEAAAKNRA.K..AL.RVT.NL.SLT.KGLSPAMSPAL.R.VSRTAS.YTD.AL.AS.
Retrocopy PGPRERLGLKIANEAAAKNRAMKHKALQRVTGNLTSLTRKGLSPAMSPALHRPVSRTASRYTDLALWASH

Parental  TPSPARSSHLKTPAGGPQTPTSTPAPGSATRTPLTQDPASITDNLLQ-LPARRKASDFF
          TPSPA.S.HLK.P..GPQTPTS.PA....T.TPLTQDPASITDNLLQ..PAR.KASDFF
Retrocopy TPSPACSTHLKNPTAGPQTPTSIPA---LTGTPLTQDPASITDNLLQ>FPARHKASDFF

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	22.38 RPM
SRP007412_cerebellum	0.00 RPM	23.84 RPM
SRP007412_heart	0.00 RPM	12.36 RPM
SRP007412_kidney	0.00 RPM	12.70 RPM
SRP007412_liver	0.00 RPM	5.08 RPM
SRP007412_testis	0.05 RPM	39.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2310 was not detected

EST

No EST(s) were mapped for retro_mmus_2310 retrocopy.

TSS

No TSS is located nearby retro_mmus_2310 retrocopy 5' end.

Lab

retro_mmus_2310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2310 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007959	2 retrocopies	retro_meug_1543, retro_meug_907,
Mus musculus	ENSMUSG00000003527	1 retrocopy	retro_mmus_2310 ,