RetrogeneDB ID: retro_mmus_2432

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:4528206..4528719(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085155
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ptp4a2
• Ensembl ID: ENSMUSG00000028788
• Aliases: Ptp4a2, Prl-2
• Description: protein tyrosine phosphatase 4a2 [Source:MGI Symbol;Acc:MGI:1277117]

Sequence

>retro_mmus_2432
ATGCATCATGTAGCCCCAGTGGAGATTTGCTATAACAACATGCGTTTTCTGATAACTCACAACCCCACTAATAGTACGAT
GCACAAGTTCACAGAGGAACTCAAGAACTACGGAGTGTCAACTTTAGTCAGAGTTTGTGATGCCACATATGATAAAACTC
TAGTTGAAAACTGTGGCATCCATGTTCTAGATCTGCCATACAACGACGGAGCCCCGCCCCCTGATGAGATCGTGGATAAT
TGGCTAGACCTGCTAAAAAACAAATTCCGTGAGGAGCCTGGTTCCTGTGTGGCAGTGCACTGTGTGGCTGGGCTAGGAAG
GGCACCCGTGCTGGTGGCACTTGCTTTGATTGAATGTGGAATGAAAAATGAAGACGCAGTTCAGTTTATCCGGCAGAAAC
GAAGGGGAGCTTTCAACTCCAAACAGCTGCTTTTTTTGGAGCACTACCGGCCTAAATTGAGGACCCGGTCACTGTCGCGC
TTCAGGGATTCTACCGTGCACTGCTGCATCCAG

Alignment

ORF - retro_mmus_2432 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          M...APVEI.Y.NMRFLITHNPTN.T..KFTEELK.YGV.TLVRVCDATYDK..VE..GIHVLD.P..DG
Retrocopy MHHVAPVEICYNNMRFLITHNPTNSTMHKFTEELKNYGVSTLVRVCDATYDKTLVENCGIHVLDLPYNDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
          APPP..IVD.WL.LLK.KFREEPG.CVAVHCVAGLGRAPVLVALALIECGMK.EDAVQFIRQKRRGAFNS
Retrocopy APPPDEIVDNWLDLLKNKFREEPGSCVAVHCVAGLGRAPVLVALALIECGMKNEDAVQFIRQKRRGAFNS

Parental  KQLLYLEKYRPKMRLR----FRDTNGHCCVQ
          KQLL.LE.YRPK.R.R....FRD...HCC.Q
Retrocopy KQLLFLEHYRPKLRTRSLSRFRDSTVHCCIQ

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	0.02 RPM	98.57 RPM
SRP007412_cerebellum	0.00 RPM	58.31 RPM
SRP007412_heart	0.00 RPM	165.27 RPM
SRP007412_kidney	0.00 RPM	127.64 RPM
SRP007412_liver	0.03 RPM	105.57 RPM
SRP007412_testis	90.88 RPM	70.03 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2432 was not detected

EST

No EST(s) were mapped for retro_mmus_2432 retrocopy.

TSS

No TSS is located nearby retro_mmus_2432 retrocopy 5' end.

Lab

retro_mmus_2432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2432 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_305

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
Callithrix jacchus	ENSCJAG00000006539	2 retrocopies	retro_cjac_3257, retro_cjac_566,
Homo sapiens	ENSG00000184007	4 retrocopies	retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Mus musculus	ENSMUSG00000026064	10 retrocopies	retro_mmus_1192, retro_mmus_1830, retro_mmus_1874, retro_mmus_1891, retro_mmus_2138, retro_mmus_2876, retro_mmus_2985, retro_mmus_3053, retro_mmus_3527, retro_mmus_575,
Mus musculus	ENSMUSG00000028788	2 retrocopies	retro_mmus_1894, retro_mmus_2432 ,
Nomascus leucogenys	ENSNLEG00000002137	3 retrocopies	retro_nleu_2880, retro_nleu_2956, retro_nleu_3015,
Oryctolagus cuniculus	ENSOCUG00000002060	1 retrocopy	retro_ocun_1673,
Otolemur garnettii	ENSOGAG00000029603	1 retrocopy	retro_ogar_3341,
Pongo abelii	ENSPPYG00000001606	3 retrocopies	retro_pabe_1507, retro_pabe_808, retro_pabe_890,
Rattus norvegicus	ENSRNOG00000050044	1 retrocopy	retro_rnor_305,
Sus scrofa	ENSSSCG00000003605	1 retrocopy	retro_sscr_1186,
Ictidomys tridecemlineatus	ENSSTOG00000002775	2 retrocopies	retro_itri_1165, retro_itri_152,
Tupaia belangeri	ENSTBEG00000006790	1 retrocopy	retro_tbel_4601,
Tursiops truncatus	ENSTTRG00000016571	2 retrocopies	retro_ttru_1396, retro_ttru_1402,