RetrogeneDB ID: retro_mmus_779

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:30906951..30907920(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084146
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pdlim1
• Ensembl ID: ENSMUSG00000055044
• Aliases: None
• Description: PDZ and LIM domain 1 (elfin) [Source:MGI Symbol;Acc:MGI:1860611]

Sequence

>retro_mmus_779
ATGACTACCCAACAGATTGTTCTCCAGGGCATGGGACCCTAGGGTTTCCACCTTGTGGGCAGCAAGGACTTTGAGCATCC
TCTTGCCATTTCCCAGGTCACTCCTAGAAGCAAGGCTGCTATAGCTAATTAATGTGTTGGAGATTTAATCACAGCCATCG
ATGGGGAAGATACCAGCAGTATGACACACTTGGAAGCTCAGAACAAAATTAAGGGCTGTGTAGACAACTTGATGCTCAGA
GTATCCACATCTGAATAGGAAATTTGGTCTCCTCTAGTGACCGAGGAGACTCATTATCCCACAAGATGAATTTAGCGTTA
GAATCCCAAGAAGTCTTGCACATAGGAAGTGCCCACAACTGAAGTGTCATGCCATTTACTGCCTCATCTGCTTCTGGCAC
CTGGGTCATCACAAACCAGTACAACAACCCAACTGGCCTCTACTCATCTGAAAACATCTCTAACTTCAACACTGCTGTGG
AGTTGAAGACCTCAGACAGTGGGGAGGAGGAGAAAAGCAGACCCTTGGTTCAGCCTCATCCTCCCAGCAGCTTTATCATT
GACAAAGAATCCAAAGTTTACAAGATGCTTAAGGAGAAGCAAGAGTTAAATGAGCCCCCCAAACAGTCCACATCTTTCCT
TTTCTGCAGGAGATCCTGGATTCAAATGGGAAAGAGGATCCCAACAAACCACCAGGATTTAGAAGTGTTAAAGCTTCAGT
CACCAAAGTGGCTGCATCCATTAGAAATGCTCAGAAGCTGCCCATCTGTGACAAATATGAAACTGGCATTGTGGGAGTGT
TGTGAAGCTGAGGGACTATCACCGCCATCCTGAATGTTAAGTGTGCACCGACTGTGGCATCAACCTGAAACAGAAGGGCC
ATTTCTTTGTAGAGGATCAGATTTACTGTGAAAAGCATTCTCAGGAGTGAATCACACCACCTGAGGGCTATGATGTGGTC
AAAGTGTTC

Alignment

ORF - retro_mmus_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTTQQIVLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAAIANLCIGDLITAIDGEDTSSMTHLEAQNKI
          MTTQQIVLQG.GP.GF.LVG.KDFE.PLAIS.VTP.SKAAIAN.C.GDLITAIDGEDTSSMTHLEAQNKI
Retrocopy MTTQQIVLQGMGP*GFHLVGSKDFEHPLAISQVTPRSKAAIAN*CVGDLITAIDGEDTSSMTHLEAQNKI

Parental  KGCADNMTLTVSRSEQKIWSPLVTEEGKRHP-YKMNLASEPQEVLHIGSAHNRSAMPFTASPAPSTRVIT
          KGC.DN..L.VS.SE..IWSPLVTEE....P..KMNLA.E.QEVLHIGSAHN.S.MPFTAS.A..T.VIT
Retrocopy KGCVDNLMLRVSTSE*EIWSPLVTEE-THYP<HKMNLALESQEVLHIGSAHN*SVMPFTASSASGTWVIT

Parental  NQYNSPTGLYSSENISNFNNAVESKTSASGEEANSRPVVQPHPSGSLIIDKDSEVYKMLQEKQELNEPPK
          NQYN.PTGLYSSENISNFN.AVE.KTS.SGEE..SRP.VQPHP..S.IIDK.S.VYKML.EKQELNEPPK
Retrocopy NQYNNPTGLYSSENISNFNTAVELKTSDSGEEEKSRPLVQPHPPSSFIIDKESKVYKMLKEKQELNEPPK

Parental  QSTSFL-VLQEILESDGKGDPNKPSGFRSVKAPVTKVAASVGNAQKLPICDKCGTGIVGVF-VKLRDHHR
          QSTSFL..LQEIL.S.GK.DPNKP.GFRSVKA.VTKVAAS..NAQKLPICDK..TGIVGV..VKLRD.HR
Retrocopy QSTSFL<FLQEILDSNGKEDPNKPPGFRSVKASVTKVAASIRNAQKLPICDKYETGIVGVL<VKLRDYHR

Parental  HPECYVCTDCGINLKQKGHFFVEDQIYCEKHARERVTPPEGYDVVTVF
          HPEC.VCTDCGINLKQKGHFFVEDQIYCEKH..E..TPPEGYDVV.VF
Retrocopy HPEC*VCTDCGINLKQKGHFFVEDQIYCEKHSQE*ITPPEGYDVVKVF

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	0.12 RPM	4.67 RPM
SRP007412_cerebellum	0.09 RPM	3.99 RPM
SRP007412_heart	0.03 RPM	38.73 RPM
SRP007412_kidney	0.19 RPM	10.16 RPM
SRP007412_liver	0.00 RPM	24.80 RPM
SRP007412_testis	0.14 RPM	3.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_779 was not detected

EST

No EST(s) were mapped for retro_mmus_779 retrocopy.

TSS

No TSS is located nearby retro_mmus_779 retrocopy 5' end.

Lab

retro_mmus_779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_779 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779 ,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,