RetrogeneDB ID: retro_mmus_269

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:140839106..140839637(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095465
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Zcchc10
• Ensembl ID: ENSMUSG00000018239
• Aliases: Zcchc10, 2410141K03Rik, AA675321, D11Ertd416e
• Description: zinc finger, CCHC domain containing 10 [Source:MGI Symbol;Acc:MGI:1196228]

Sequence

>retro_mmus_269
ATGGTGACTCCCATGCAGAGGTTCATAGATCCGAGGCAAGCTGGAGCCAATAAGCAACGTGTAAGATATCAGAAATGCTT
GAAATTTGGACATCGGGCTTATGAATGCAAAGGGAAAAGAAAGTACCTACACTGGCCTTCTAGAACAGCAGAGCTGAAGA
AAGCTTTAGAAGAAAAAGAAAATATTTATTGCAGCAAAGCATCAGAGACCAACATAGAGAGAAAGACTGAGAAGAGGAGA
TCTAAGGATGTAACTTCCAGTACCTCTAGAAGTGACAGTTCGGCCTGCGAGTCTTCATCAGAGAATGAGACATCTGCCTC
ATCCTCTTCAGAAGACAGTGACCCAGGTGCAAGCCTCTCTAGCTCCTCCTCCTCCTCTTCCTCCTCATCTTTGTCCTTGG
ACTCAGACTCAGACTCCAGCTCCTCCAGCTCCTCCAGCTCCTCCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAAC
AACAACAGCAGCAGTACCGAGGCAGCTCTGATGATGAGACACCGAAGAAGA

Alignment

ORF - retro_mmus_269 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 93.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATPMHRLIARRKAEANKQHVRCQKCLEFGHWTYECKGKRKYLHRPSRTAELKKALKEKENRLLLQSIGE
          M.TPM.R.I..R.A.ANKQ.VR.QKCL.FGH..YECKGKRKYLH.PSRTAELKKAL.EKEN........E
Retrocopy MVTPMQRFIDPRQAGANKQRVRYQKCLKFGHRAYECKGKRKYLHWPSRTAELKKALEEKEN-IYCSKASE

Parental  TNIEKKIKKKKRSKSVTSSSTSSSDSSASESSSESETSASSSSEDSDSDESLSSSSSSSSSSACSSSSSS
          TNIE.K...K.RSK.VT.SSTS.SDSSA.ESSSE.ETSASSSSEDSD...SLSSSSSSSSSS..S..S.S
Retrocopy TNIERK-TEKRRSKDVT-SSTSRSDSSACESSSENETSASSSSEDSDPGASLSSSSSSSSSSSLSLDSDS

Parental  SSSSSSSDSDSSSSSSSSSSSSESSS
          .SSSSSS.S.SSSSSSSSSSSS...S
Retrocopy DSSSSSSSSSSSSSSSSSSSSSNNNS

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	5.12 RPM
SRP007412_cerebellum	0.00 RPM	5.99 RPM
SRP007412_heart	0.00 RPM	3.14 RPM
SRP007412_kidney	0.00 RPM	3.93 RPM
SRP007412_liver	0.00 RPM	2.43 RPM
SRP007412_testis	0.00 RPM	3.52 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_269 was not detected

EST

No EST(s) were mapped for retro_mmus_269 retrocopy.

TSS

No TSS is located nearby retro_mmus_269 retrocopy 5' end.

Lab

retro_mmus_269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_269 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031203	1 retrocopy	retro_cfam_643,
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132, retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269 ,
Otolemur garnettii	ENSOGAG00000032171	1 retrocopy	retro_ogar_3011,
Pongo abelii	ENSPPYG00000015776	1 retrocopy	retro_pabe_2395,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037, retro_rnor_2528, retro_rnor_801,
Sorex araneus	ENSSARG00000007221	1 retrocopy	retro_sara_639,