RetrogeneDB ID: retro_ocun_940

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:39670386..39671024(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMMDC1
• Ensembl ID: ENSOCUG00000009500
• Aliases: None
• Description: translocase of inner mitochondrial membrane domain containing 1 [Source:HGNC Symbol;Acc:1321]

Sequence

>retro_ocun_940
GTCACTCACTCACTCCTGCAGTTATCCTCAGTCCATCACATGTCACCTGCTGGCGGTCCTGGGGCCTTGAGCGCCCAAGT
GTGTCTGCCCCAAGATCGGGAGAGGGCAATGGAGGTGCCGCCGCCGGCTCCGTGGAGCTTCCTTTACCGAACCCTGGGTC
CATTTCCCCGAGTCTTTGCGGCTGAGAATGTGGCTGCCGATTCGGAAGCCCTGGCAGAGAATGGGAAGCTGCCTTCCTAC
GTCCCCGAACGCTATTACCCGGAACCGGATGGGACCGTCTCCGGGAGCTGTTGTTAAAGAGTAAAATGAACAGCAGAGGA
CGTCAAAGGAGCTTGAGAATATCTATAGGGCGGCAATTTCAGCAGGCATCATTGGCTGGGCTTATGGTAGAATACCAGCT
TTTATTCATGCTAAAAAAATGCTACATTGAGCAGAGCCAGGCACAAATTTATCACAACCGGTTTGATGCTGTGCAAAGTG
CTCACCCCGCTGCCACGCGAGGTTTCGTTCGGTACGGCTGGCGCTGGAGCTGGAGACCCGCGGTGTTCGTGACCATATTC
AACACAGTGAACACTAGTCTAAATGTGTACCGAAATAAAAATGCCCTAAGCCATTTTGTCATTGCAGGGGGTAAGACA

Alignment

ORF - retro_ocun_940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHSLVQLSSARRMSPAGGPGALSAQVCLPQDRERAMEVPPPAPRSFLYRALGPFPRVFAAENVAADSEA
          ..HSL.QLSS...MSPAGGPGALSAQVCLPQDRERAMEVPPPAP.SFLYR.LGPFPRVFAAENVAADSEA
Retrocopy VTHSLLQLSSVHHMSPAGGPGALSAQVCLPQDRERAMEVPPPAPWSFLYRTLGPFPRVFAAENVAADSEA

Parental  LAENRKLPSYVPERYYPE-SGWDRLRELF-VKD--EQQRTSKELENIYRAAISAGIIGWAYGGIPAFIHA
          LAEN.KLPSYVPERYYPE..GWDRLREL..VK...EQQRTSKELENIYRAAISAGIIGWAYG.IPAFIHA
Retrocopy LAENGKLPSYVPERYYPE<TGWDRLRELL<VKE*NEQQRTSKELENIYRAAISAGIIGWAYGRIPAFIHA

Parental  KKS-YIEQSQAQIYHNRFDAVQSAHRAATRGFIRYGWRWSWRTAVFVTIFNTVNTSLNVYRNKNALSHFV
          KK..YIEQSQAQIYHNRFDAVQSAH.AATRGF.RYGWRWSWR.AVFVTIFNTVNTSLNVYRNKNALSHFV
Retrocopy KKM>YIEQSQAQIYHNRFDAVQSAHPAATRGFVRYGWRWSWRPAVFVTIFNTVNTSLNVYRNKNALSHFV

Parental  IAGAVT
          IAG..T
Retrocopy IAGGKT

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	18.65 RPM
SRP017611_kidney	0.00 RPM	24.12 RPM
SRP017611_liver	0.00 RPM	9.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_940 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_940 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002519	1 retrocopy	retro_etel_1905,
Macropus eugenii	ENSMEUG00000003777	1 retrocopy	retro_meug_1317,
Monodelphis domestica	ENSMODG00000018197	2 retrocopies	retro_mdom_1842, retro_mdom_419,
Oryctolagus cuniculus	ENSOCUG00000009500	1 retrocopy	retro_ocun_940 ,