RetrogeneDB ID: retro_mmus_1894

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:23235235..23235736(+)
• Located in intron of: ENSMUSG00000026774

Retrocopy information

• Ensembl ID: ENSMUSG00000084098
• 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_1894
ATGAACCGTCCAGCCCCTGTGGAGATCTCTTATGAGAACATGAGTTTTCTGATAACTCACAACCCCACCAATGCGACTCT
CAACAAGTTCACATAGGAACTTAAGAAGTACGGAGTAACAACTTTGGTTCGAGTTTGTGATGCTACATATGATAAAGCTC
CAGTTGAAAAAGAAGGAATCCACGTTCTAGATTGGCCGTTTGATGATGGAGCTCCACCCTCTAATCAGATAGTAGATGAT
TGGCTAAACCTGTTAAAAATCAAATTTCGTGAAGAGCTAGGCTCTTGTGTTGCAGTGCATTGTGTTTCAGGATTGGGAAG
GGCTCCTGTGCTAGTCGCACTTGCATTGATTGAATGCGGAATGAAGTACGAAGATGCTGTTCAATTCATAAGACAAAAAA
GAAGAGGAGCATTCAATTCCAAACAGCTGCTTTACTTGGAGAAGTACCGACCTAAGAAGCGATTACGCTTCAGAGATACC
AATGGGCACTGCTGTGTTCAG

Alignment

ORF - retro_mmus_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          MNRPAPVEISYENM.FLITHNPTNATLNKFT.ELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
Retrocopy MNRPAPVEISYENMSFLITHNPTNATLNKFT*ELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
          APP.NQIVDDWLNLLK.KFREE.G.CVAVHCV.GLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
Retrocopy APPSNQIVDDWLNLLKIKFREELGSCVAVHCVSGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS

Parental  KQLLYLEKYRPKMRLRFRDTNGHCCVQ
          KQLLYLEKYRPK.RLRFRDTNGHCCVQ
Retrocopy KQLLYLEKYRPKKRLRFRDTNGHCCVQ

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	98.57 RPM
SRP007412_cerebellum	0.04 RPM	58.31 RPM
SRP007412_heart	0.09 RPM	165.27 RPM
SRP007412_kidney	0.12 RPM	127.64 RPM
SRP007412_liver	0.11 RPM	105.57 RPM
SRP007412_testis	0.96 RPM	70.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1894 was not detected

EST

No EST(s) were mapped for retro_mmus_1894 retrocopy.

TSS

No TSS is located nearby retro_mmus_1894 retrocopy 5' end.

Lab

retro_mmus_1894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1894 has 0 orthologous retrocopies within eutheria group .

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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,