RetrogeneDB ID: retro_ocun_1136

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:30639625..30640256(+)
• 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_1136
AATGCTCCAGGGAAATACAAGGAAAGAATAGGGCACAGGTATACTGAGATCTTCACAAGTAGCAGGCGTAACATCAAGGA
TTTTGTGATCCCCGAAGAAGACTGCTGGGACAGAGACCAGGACCATGTGATAGACCAATAGGAGGGAGAGGGGGTTATTC
TGGAGCTGGGCCTGGGAGTACGTTTGACAGAGTGCGACGAGGAGGTGATGGATATGATGGTGGCTAGGGAGCTTTGAATG
ACTGTGGTGGCTATAATAATATGGCTATGGAAATGATGGCTTTGATGACAGAATGAGAGATGGATGAGGTATGGGAGGAC
ATGGCTACGGTAGAGCTGGTGATGCCAATTCAGGTTTTCATGGTGGTCATTTTATACAGATAAAAGGGCTGCCGTTTCTT
GCAACTGATATTGCTAATTTCCTCTTACCACTAAATCCAATACAAGTTCATATGGATATAGGGGCTGATGGCAGAGCAAC
AGGAGAAGAGGATGTCGAGTTTGTGGCACATGCAGATGCAGTAGCTGCCACGTCTAGAGATAAAAATAATATGCGACATC
AATACGCTGAACTCTTCTCCAATTCTGCTCCTGGTGACGGCTCTGGAATGGGAGGCTACGGCAGAGGTGGA

Alignment

ORF - retro_ocun_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.67 %
• Parental protein coverage: 61.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NALGKHKERIGHRYIEIFRSSRSEIK-GFYDPPRRLLGQRPGPYDRPIGGRGGYYGAGRGSMYDRMRRGG
          NA.GK.KERIGHRY.EIF.SSR..IK.GF.DP.RRLLGQRPGP.DRPIGGRGGY.GAG.GS..DR.RRGG
Retrocopy NAPGKYKERIGHRYTEIFTSSRRNIK<GFCDPRRRLLGQRPGPCDRPIGGRGGYSGAGPGSTFDRVRRGG

Parental  DGYDGGYGGFDDYGGYNN-YGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATEN
          DGYDGG.G...D.GGYNN.YGYGNDGFDDRMRDG.GMGGHGYG.AGDA.SGFHGGHF....GLPF.AT..
Retrocopy DGYDGG*GALNDCGGYNN<YGYGNDGFDDRMRDG*GMGGHGYGRAGDANSGFHGGHFIQIKGLPFLAT--

Parental  DIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNSTPGGGSGMGG
          DIANF..PLNPI.VH.DIGADGRATGE.DVEFV.H.DAVAA.S.DKNNM.H.Y.ELF.NS.PG.GSGMGG
Retrocopy DIANFLLPLNPIQVHMDIGADGRATGEEDVEFVAHADAVAATSRDKNNMRHQYAELFSNSAPGDGSGMGG

Parental  SGMGG
          .G.GG
Retrocopy YGRGG

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_1136 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1136 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,