RetrogeneDB ID: retro_rnor_305

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:22178062..22178578(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000009002
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSRNOG00000050044
• Aliases: None
• Description: Protein tyrosine phosphatase type IVA 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6P9X4]

Sequence

>retro_rnor_305
ATGAACCATGTAGCCCCAGTGGAGATCTGCTACGACAGCATGCGTTTTCTGATAACTTACAACCCCACCAATGAGACGAT
ACATAAGTTCACAGAGGAACTTAAGAGCTACGGAGTGACAACCTTAGTCAGAGTTTGTGACGCCACATATGATAAGACTC
TAGTTGAAAACAGTGGCATCCGTGTTCTAGACCTGCCCTACAGTGATGGAGCGCCGCCCCCTGATGAGCTAGTGGATAAT
TGGCTAGACCTGCTAAAAAACAAATTCCGTGAGGAGCCTGGTTGCTGTGTGGCAGTGCACTGTATGGCTGGGCTCGGAAG
GGCGCCTGTGCTGGTGGCACTTGCTTTGATCGAGTGTGGAATGAAGAATGAAGACGCAGTTCACTTAATCCGGCAGAAAC
GAAGGGGCGCTTTCAACACCAAACAGCTGCTTTTTTTGGAGCACTACCGTCCCAAGATGAGGCCCCGAACACGATCACGC
TTCAAGGATTCCACGGTGTACTGTTGCATCCAATAG

Alignment

ORF - retro_rnor_305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          MN..APVEI.Y..MRFLIT.NPTN.T..KFTEELK.YGVTTLVRVCDATYDK..VE..GI.VLD.P..DG
Retrocopy MNHVAPVEICYDSMRFLITYNPTNETIHKFTEELKSYGVTTLVRVCDATYDKTLVENSGIRVLDLPYSDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
          APPP...VD.WL.LLK.KFREEPGCCVAVHC.AGLGRAPVLVALALIECGMK.EDAV..IRQKRRGAFN.
Retrocopy APPPDELVDNWLDLLKNKFREEPGCCVAVHCMAGLGRAPVLVALALIECGMKNEDAVHLIRQKRRGAFNT

Parental  KQLLYLEKYRPKMRLR----FRDTNGHCCVQ
          KQLL.LE.YRPKMR.R....F.D....CC.Q
Retrocopy KQLLFLEHYRPKMRPRTRSRFKDSTVYCCIQ

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
SRP017611_brain	0.00 RPM	64.49 RPM
SRP017611_kidney	0.00 RPM	114.16 RPM
SRP017611_liver	0.00 RPM	32.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_305 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_305 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2432

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 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	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	ENSRNOG00000011771	4 retrocopies	retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus	ENSRNOG00000046370	4 retrocopies	retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
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,