RetrogeneDB ID: retro_mmus_1958

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:104820178..104820930(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083856
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tardbp
• Ensembl ID: ENSMUSG00000041459
• Aliases: Tardbp, 1190002A23Rik, C85084, TDP-43, Tdp43
• Description: TAR DNA binding protein [Source:MGI Symbol;Acc:MGI:2387629]

Sequence

>retro_mmus_1958
GAAATACCATCAGAAGACGATGGGACAGTGTTGCTGTCCACAGTTACAGCCCAGTTTCCAGGGGCATGTGGCCTGTGCTA
CTGGAATCCAGTGTCTCAGTGTATGAGAGGTGTCCAACTGGTGGAAGGAATTCTGCATGCCCCAGATGCTGGCTGGGGCA
ATCTGGTATATGTTGTCAACTATCCCAAAGATAACAAAAGGAAAATAGATGAGACGGATGCTTCCTCTGCAGTGAAAGTG
AAAAGAGCAGTCCAGAAAATGTCTGATCTCATAGTATTGGGTCTCCCTGGAAAACAACAGAACAGGTTCTGAAAGACTAT
TTCAGTACTTTCGGAGAGGTTCTTATGGTTCGGGTCAAGAAAGATCTTAAAACTTGCCACTCAGAAGGGTTTGACTTTGT
TCGATTTACAGAATATGAAACCCAAGTGGAAGTAATGTCACAACGACATATGATAGATGGGCGACGGTGTGACTGTAAAC
TTCCGAACTCTAAGCAAAGCCCAGATGAGCCTTTGAGAAGCAGAAAGGTGTTTGTTGGAGGTTGTACAGAGGACATGACT
GCTGAAGCTCTTCTGCAGTATGGAGAAGTGGTAGATGTCTTCATTCCCAAACCATTCAGAACTTTTGCCTTCGTTACCTT
TGCAGATGATAAGGTTGTCCAGTCTCTTTGTGGAGAGGATTTGATCATTAAAGGACTCAGCGTGCATATATCCAGTGCTG
AACCTAAGCATAATAGCAATAGACAGAAAGAA

Alignment

ORF - retro_mmus_1958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.84 %
• Parental protein coverage: 86.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMD
          EIPSEDDGTVLLSTVTAQFPGACGL.Y.NPVSQCMRGV.LVEGILHAPDAGWGNLVYVVNYPKDNKRK.D
Retrocopy EIPSEDDGTVLLSTVTAQFPGACGLCYWNPVSQCMRGVQLVEGILHAPDAGWGNLVYVVNYPKDNKRKID

Parental  ETDASSAVKVKRAVQKTSDLIVLGL-PWKTTEQDLKDYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY
          ETDASSAVKVKRAVQK.SDLIVLGL.PWKTTEQ.LKDYFSTFGEVLMV.VKKDLKT.HS.GF.FVRFTEY
Retrocopy ETDASSAVKVKRAVQKMSDLIVLGL<PWKTTEQVLKDYFSTFGEVLMVRVKKDLKTCHSEGFDFVRFTEY

Parental  ETQVKVMSQRHMIDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP
          ETQV.VMSQRHMIDGR.CDCKLPNSKQSPDEPLRSRKVFVG.CTEDMTAE.L.Q.....GEVVDVFIPKP
Retrocopy ETQVEVMSQRHMIDGRRCDCKLPNSKQSPDEPLRSRKVFVGGCTEDMTAEALLQY----GEVVDVFIPKP

Parental  FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHNSNRQLE
          FR.FAFVTFADDKV.QSLCGEDLIIKG.SVHIS.AEPKHNSNRQ.E
Retrocopy FRTFAFVTFADDKVVQSLCGEDLIIKGLSVHISSAEPKHNSNRQKE

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	0.07 RPM	146.56 RPM
SRP007412_cerebellum	0.09 RPM	188.10 RPM
SRP007412_heart	0.06 RPM	74.34 RPM
SRP007412_kidney	0.13 RPM	141.52 RPM
SRP007412_liver	0.05 RPM	73.54 RPM
SRP007412_testis	0.05 RPM	99.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1958 was not detected

EST

No EST(s) were mapped for retro_mmus_1958 retrocopy.

TSS

No TSS is located nearby retro_mmus_1958 retrocopy 5' end.

Lab

retro_mmus_1958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1958 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
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958 ,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,