RetrogeneDB ID: retro_ocun_1615

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018717:2731231..2731804(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSOCUG00000004443
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_ocun_1615
GGCGGCTATAATAACTATGGCTATGGAAATGATAGCTTTGATGACAGAATGAGAGATGGAGGTGGCATGAGAGGGCATGG
CTCTTGGGGAGCTGGTGATGCAAGTTCAGGGTTTTATGGTGGTCATTTTGTATATATGAGAGCATTACTTTTTTATGCAA
CTGAAAATGACATTGCTATTTTCTTCTCACCACTGAATCCAGTACAAGTTCATCGTGATATTGGAGCTGATGCCAAAGCA
ACGGGAGAAGCAAACGTAGAGTTCGTGATACGTGAAGACTCAGTAGCTGCCATATCTAAAGATAAAAATAGTGTGCAACA
TCGATGCATAGAACTCGTCCTGAAGTCTACTGGCAGCTCTGGCTTGGGAGGTTCTGGAATGGGAGGCTACGGCAGAGATG
GAATGGGTAATCGGGGAGGGTATGGATCTGTTGGAAGAATGGGGATGGGGAACAATGACCGTGGAGGATACGGCCCTCCT
GATGGCTTGGGTGGTTATGGCCATGGTGGTGGAGGCAGTGGACGGTACTAGGGACAAGGCAGCTTGAGTGGAGGTGGGTG
GTGTGGGACGTAC

Alignment

ORF - retro_ocun_1615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.24 %
• Parental protein coverage: 55.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFFSPLNPIRV
          GGYNNYGYGND.FDDRMRDG.GM.GHG..GAGDASSGF.GGHFV.MR.L.F.ATENDIA.FFSPLNP..V
Retrocopy GGYNNYGYGNDSFDDRMRDGGGMRGHGSWGAGDASSGFYGGHFVYMRALLFYATENDIAIFFSPLNPVQV

Parental  HIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNSTPGGGSGMGGSGMGGYGRDGMDNQ
          H.DIGAD..ATGEA.VEFV..ED.VAA.SKDKN..QHR.IEL.L.ST..G.SG.GGSGMGGYGRDGM.N.
Retrocopy HRDIGADAKATGEANVEFVIREDSVAAISKDKNSVQHRCIELVLKST--GSSGLGGSGMGGYGRDGMGNR

Parental  GGYGSVGRMGMGNNYSGGYGTPDGLGGYGRGGGGSGGYYGQGGMSGGGWRGMY
          GGYGSVGRMGMGNN..GGYG.PDGLGGYG.GGGGSG.Y.GQG..SGGGW.G.Y
Retrocopy GGYGSVGRMGMGNNDRGGYGPPDGLGGYGHGGGGSGRY*GQGSLSGGGWCGTY

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	148.90 RPM
SRP017611_kidney	0.00 RPM	143.93 RPM
SRP017611_liver	0.00 RPM	117.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1615 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1615 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615 ,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,