RetrogeneDB ID: retro_ocun_1204

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:104069400..104069837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DHRS11
• Ensembl ID: ENSOCUG00000021228
• Aliases: None
• Description: dehydrogenase/reductase (SDR family) member 11 [Source:HGNC Symbol;Acc:28639]

Sequence

>retro_ocun_1204
ATGGCCAGGGCCAGCATGGACCAGTGGTGTGACCGACTGTCACAGATGTCAGGAACCTCAGGGGACATGGGTGTGACAGT
GGCCCAGGTGCTGGTCCAGCAGGGCTTGAAGGTGGTGGATTGTGCTTACACAAGGGACAAATCTAGGAACTGGCCACAGA
ATTTAAGAGGGCAGCCTATGCTACGACTTTGATCTCCTACAAATGAGACCAGTACAATGAGCAGAACATCACTGCTGGAT
TCTTAGATAGCTGCTCGCAGCACAGCAGTGTGGTAATCTCCATCAAGAATGGCAGCTTGGCCTGGCCTGACACCTTACTC
TCAGGCAGCATCTGTGGCTGGAAGGACATATTCAGTGTCATCATGCCCACCATGAGCATCTGCACCTGAGAAGCCTACTG
GTCCATGAAGGAGTGCAGCATGGATGATGGCACAGTG

Alignment

ORF - retro_ocun_1204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.7 %
• Parental protein coverage: 55.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARAGMERWRDRLALVTGASVGIGAAVARALVQQGLKV-GCART-VGNIEELAAECKSAGYPGTLVPFRC
          MARA.M..W.DRL....G.S...G..VA..LVQQGLKV..CA.T..G.I.ELA.E.K.A.Y..TL.....
Retrocopy MARASMDQWCDRLSQMSGTSGDMGVTVAQVLVQQGLKVVDCAYT<KGQI*ELATEFKRAAYATTLISYK*

Parental  DLSNEEDILSMFSAIRSQHGGVDICINNAGFARPDTLLDGSTSGWKDMFNVNVLALSICTREAYQSMKER
          D..NE..I...F....SQH..V.I.I.N...A.PDTLL.GS..GWKD.F.V.....SICT.EAY.SMKE.
Retrocopy DQYNEQNITAGFLDSCSQHSSVVISIKNGSLAWPDTLLSGSICGWKDIFSVIMPTMSICT*EAYWSMKEC

Parental  GVDDGHI
          ..DDG..
Retrocopy SMDDGTV

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	85.32 RPM
SRP017611_kidney	0.00 RPM	95.88 RPM
SRP017611_liver	0.00 RPM	94.42 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1204 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001031	2 retrocopies	retro_cjac_3276, retro_cjac_3277,
Oryctolagus cuniculus	ENSOCUG00000021228	1 retrocopy	retro_ocun_1204 ,