RetrogeneDB ID: retro_ocun_1379

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:125614825..125615365(-)
• 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_1379
TTTGATGACAGAATGAGAGATGGAAGAGGTGTGGGAGGAAGTGCCTATGGTGGGGCTGGTGATGCAAGGTCAGGTTTTCA
TGGTGGTCATTTTGTACATATGAGAGGCCTGCCTTATTGTGCAATTGAAAATGACATTGCTAATTTCTTCTCACCACTAA
ATCCAATATGAGTTCATATTGATATTGGAGCTGATGGCAGAGCAACGGGAGAAGCAGATGCAGAGCTTGTGACACATGAA
GATGCAGTAGCTGCCATGTCTAAAGATAAAAATAATATGCAACATCGATACATTGAACTCTTCTTGAATTCTACGCCTGG
CGGTGACTCTGGAATGGGAGGTTCTGGAATGGGAGGCTACAGCAGAGATGGAATGGATAATCAGGAAGGATATGGATCTG
TTGGAAGAATAGGAATGGGAAACAATTACAGTGGAGGATATGGTACTCCTGATGGATTGGGTGGTTATGGCCATGGTGGT
GGAAGTGGAGGTTACTATGGGCAAGGTGGCATGAGTGGAGGTGGATGGTGTGGGATGTAC

Alignment

ORF - retro_ocun_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 52.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATG
          FDDRMRDGRG.GG..YGGAGDA.SGFHGGHFVHMRGLP..A.ENDIANFFSPLNPI.VHIDIGADGRATG
Retrocopy FDDRMRDGRGVGGSAYGGAGDARSGFHGGHFVHMRGLPYCAIENDIANFFSPLNPI*VHIDIGADGRATG

Parental  EADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNSTPGGGSGMGGSGMGGYGRDGMDNQGGYGSVGRMGMG
          EAD.E.VTHEDAVAAMSKDKNNMQHRYIELFLNSTPGG.SGMGGSGMGGY.RDGMDNQ.GYGSVGR.GMG
Retrocopy EADAELVTHEDAVAAMSKDKNNMQHRYIELFLNSTPGGDSGMGGSGMGGYSRDGMDNQEGYGSVGRIGMG

Parental  NNYSGGYGTPDGLGGYGRGGGGSGGYYGQGGMSGGGWRGMY
          NNYSGGYGTPDGLGGYG..GGGSGGYYGQGGMSGGGW.GMY
Retrocopy NNYSGGYGTPDGLGGYGH-GGGSGGYYGQGGMSGGGWCGMY

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	0.06 RPM	148.90 RPM
SRP017611_kidney	0.00 RPM	143.93 RPM
SRP017611_liver	0.15 RPM	117.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1379 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1379 has 0 orthologous retrocopies within eutheria group .

---

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,