RetrogeneDB ID: retro_mmus_2112

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:155427283..155427923(-)
• Located in intron of: ENSMUSG00000038369

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl8
• Ensembl ID: ENSMUSG00000003970
• Aliases: None
• Description: ribosomal protein L8 [Source:MGI Symbol;Acc:MGI:1350927]

Sequence

>retro_mmus_2112
TATACTAAGGGTACCATGAAGGACATCCATTACCTTGTCTGCTGCTCTCCCTTTGTGAATGTGGTCCTTCATGTTCCCTA
CTGATTTAAGAATCAGATGGAGCTAGTTATAGCTACAGAGAGAATCCACACTGGACAGTTTGTGTACTGCAGCAAAATGT
CCAGCTCAGTATCAGCAGTGTTTTCTCTGTGGGCACCATGCCTGAGTGTACTATTGTGTTTTCTGGGGACATGCCTGGAG
ACAGAGGCAAGTTTGTGTGAACCCTTGAGAACTATGCCATAGTCATCTCCCACACCCAAAGACCAAGAAGACCTAGGTAA
AGCTGCCTTCAGGGTCTAAGGTCATTTTTGAGGCCAACAGAGCTATTATTGGTATGGTGGCCAGTGGGGGTAGAATTGAC
AAACCTATCTTAAACATGAGCCCTGCATACTACAAGTAAAAGGCAAGAGGAATTGCTAGCTACATATGCAGGGTGTGGCC
ATAGATCCTGTGGAACATCCCTTTGGAGGCTATGACCACCAGTACATTAGCAACCCTCCACTATCCAGAGAGATGTCCCT
GCTGGGCACAAAGTGGTTCTCATTGCTGCCCACTATACTGGGCGACTACATGGAACCAAAAACTGCAGAAGAAAGAAAAC

Alignment

ORF - retro_mmus_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.54 %
• Parental protein coverage: 84.82 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YIKGIVKDIIHDPGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKA-QLNIGNVLPVGTMP
          Y.KG..KDI.H......P...VV...PY.FK...EL.IA.E.IHTGQFVYC.K...QL.I..V..VGTMP
Retrocopy YTKGTMKDI-HYLVCCSPFVNVVLHVPY*FKNQMELVIATERIHTGQFVYCSKMS<QLSISSVFSVGTMP

Parental  EGTIVCCLEEKPGDRGKLARASGNYATVISH-NPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDK
          E.TIV......PGDRGK......NYA.VISH..P.TKKT.VKLPSGSK.VI..ANRA..G.VA.GGRIDK
Retrocopy ECTIVFS-GDMPGDRGKFV*TLENYAIVISH<HPKTKKT*VKLPSGSK-VIFEANRAIIGMVASGGRIDK

Parental  PILKAGRAYHKYKA-KRNCWPRVRGVAMNPVEHPFGGGNHQHIG-KPSTIRRDAPAGRKVGLIAARRTGR
          PIL....AY.K.KA.KRNC.....GVA..PVEHPFGG..HQ.I...PSTI.RD.PAG.KV.LIAA..TGR
Retrocopy PILNMSPAYYK*KA<KRNC*LHMQGVAIDPVEHPFGGYDHQYIS<QPSTIQRDVPAGHKVVLIAAHYTGR

Parental  LRGTKT-VQEKEN
          L.GTK...Q.KEN
Retrocopy LHGTKN<LQKKEN

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	123.99 RPM
SRP007412_cerebellum	0.04 RPM	178.07 RPM
SRP007412_heart	0.00 RPM	251.66 RPM
SRP007412_kidney	0.02 RPM	251.61 RPM
SRP007412_liver	0.03 RPM	224.72 RPM
SRP007412_testis	0.05 RPM	201.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2112 was not detected

EST

No EST(s) were mapped for retro_mmus_2112 retrocopy.

TSS

No TSS is located nearby retro_mmus_2112 retrocopy 5' end.

Lab

retro_mmus_2112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Gorilla gorilla	ENSGGOG00000008164	1 retrocopy	retro_ggor_1974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Mus musculus	ENSMUSG00000003970	2 retrocopies	retro_mmus_2004, retro_mmus_2112 ,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Pan troglodytes	ENSPTRG00000020716	1 retrocopy	retro_ptro_1931,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,