RetrogeneDB ID: retro_ocun_1673

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018757:1493897..1494240(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSOCUG00000002060
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_ocun_1673
ATGAATTATCCAGCCCCCTGTAGAGATCTCCCATGAGAACACGCATTTTCTGTTAGTTCACAACCCTGCCAATGCCACTT
TCAACAAGGTCAGAGAGGAACTTAAAAAACATGGAATGACATCTTTGGTTTGTGATGCTACATATGATCAAGTTACAGTT
GAAAAAGAAAGAATCCTCATTCTAGGTTGATCATTTGATGATGGAGCTCCACCCCCTATTCATTTAGTTAGGGGACTGAC
AAGCCTGTTAAAAACCACGTTTCCTGAAGAGCCAGGTCGATGTGTTGCAGTGCATCCTGTTGCAGGATTGGGGAAGGCAC
CTGTGTTAATTACACTTACATTG

Alignment

ORF - retro_ocun_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.25 %
• Parental protein coverage: 69.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNRPAP-VEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDAPYDKAPVEKEGIHVLDWPFDD
          MN.PAP.VEIS.EN..FL..HNP.NAT.NK..EELKK.G.T.LV..CDA.YD...VEKE.I..L...FDD
Retrocopy MNYPAP>VEISHENTHFLLVHNPANATFNKVREELKKHGMTSLV--CDATYDQVTVEKERILILG*SFDD

Parental  GAPPPNQIVDDWLNLLKNKFREEPGCCVAVHCVAGLGRAPVLVALAL
          GAPPP...V.....LLK..F.EEPG.CVAVH.VAGLG.APVL..L.L
Retrocopy GAPPPIHLVRGLTSLLKTTFPEEPGRCVAVHPVAGLGKAPVLITLTL

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	31.84 RPM
SRP017611_kidney	0.00 RPM	36.89 RPM
SRP017611_liver	0.00 RPM	14.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1673 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1673 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1673 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 28 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 ,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
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,