RetrogeneDB ID: retro_ocun_953

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:64844663..64845648(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027427
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM49B
• Ensembl ID: ENSOCUG00000013690
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]

Sequence

>retro_ocun_953
AGGTACCTTAACATGGGGAATCTTCTTAAAGTTTTGACATGCACAGACCTTGAGCAGGGGCCAAATTTTTTTCCTTGATT
TTGAAAATGCCCAGCCTACAGAGTCTGAGAAGGAAATTTATAATCAGGTGAATGTAGTCTTAAAAGATGCAGAAGGCATC
TTGGAAGACTTGCAGTCATACAGAGGAGCTGGCCATGAAATACGTGAGGCAATCCAGCATCCAGCAGATGAGAAGTTGCA
AGAGAAGGCATGGGGTGCCGTTGTTCCACTAGTAGGCAAATTAAAGAAATTTTATGAATTTTCTCAGAGGTTAGAAGCAG
CACTACGAGGTCTTTTGGGAGCCTTGACAAGTACCCCGTACTCTCCCACCCAGCATTTAGAGCAAGAGCAGGCTCTTGCT
AAACAGTTTGCAGAAATTCTTCATTTTACACTCCGGTTTGATGAACTCAAGATGACGAATCCTGCCATACAGAACGATTT
CAGTTATTACAGAAGAATGTTGAGTCGGATGAGGATTAATAATGTTCCAGCAGAAGGAGAAAATGAAGTAAATAATGAAT
TGGCAAATCGAATGTCTTTGTTTTATGCTGAGGCAACCCCAATGCTGAAAACATTAAGTGATGCCATGACAAAATTTGTC
TCAGAGAATAAAAATTTACCAATAGAAAATACCACAGATTGTCTAAGCACCATGGCTAGTGTTTGCAGAGTCATGCTTGA
AACACCAGAATACAGAAGCAGGTTTACAAATGAAGAAACAGTATCCTTCTGCTTGAGAGTAATGGTGGGTCTTATCATCC
TCTATGACCATGTGCATCCAGTAGGAGCATTTGCCAAAACCTCCAAAATTGATATGAAAGGTTGTATCAAAGTTCTTAAG
GACCAGCCTCCCAACAGTGTAGAAGGTCTTCTAAATGCTCTCAGGTACACAACAAAACATTTGAATGATGAGACTACCTC
CAAGCAAATTAAATCCATGCTGCAG

Alignment

ORF - retro_ocun_953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.48 %
• Parental protein coverage: 96.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RYLNMGNLLKVLTCTDLEQGPN-FFLDFENAQPTESEKEIYNQVNVVLKDAEGILEDLQSYRGAGHEIRE
          RYLNMGNLLKVLTCTDLEQGPN.FFLDFENAQPTESEKEIYNQVNVVLKDAEGILEDLQSYRGAGHEIRE
Retrocopy RYLNMGNLLKVLTCTDLEQGPN>FFLDFENAQPTESEKEIYNQVNVVLKDAEGILEDLQSYRGAGHEIRE

Parental  AIQHPADEKLQEKAWGAVVPLVGKLKKFYEFSQRLEAALRGLLGALTSTPYSPTQHLEREQALAKQFAEI
          AIQHPADEKLQEKAWGAVVPLVGKLKKFYEFSQRLEAALRGLLGALTSTPYSPTQHLE.EQALAKQFAEI
Retrocopy AIQHPADEKLQEKAWGAVVPLVGKLKKFYEFSQRLEAALRGLLGALTSTPYSPTQHLEQEQALAKQFAEI

Parental  LHFTLRFDELKMTNPAIQNDFSYYRRTLSRMRINNVPAEGENEVNNELANRMSLFYAEATPMLKTLSDAT
          LHFTLRFDELKMTNPAIQNDFSYYRR.LSRMRINNVPAEGENEVNNELANRMSLFYAEATPMLKTLSDA.
Retrocopy LHFTLRFDELKMTNPAIQNDFSYYRRMLSRMRINNVPAEGENEVNNELANRMSLFYAEATPMLKTLSDAM

Parental  TKFVSENKNLPIENTTDCLSTMASVCRVMLETPEYRSRFTNEETVSFCLRVMVGVIILYDHVHPVGAFAK
          TKFVSENKNLPIENTTDCLSTMASVCRVMLETPEYRSRFTNEETVSFCLRVMVG.IILYDHVHPVGAFAK
Retrocopy TKFVSENKNLPIENTTDCLSTMASVCRVMLETPEYRSRFTNEETVSFCLRVMVGLIILYDHVHPVGAFAK

Parental  TSKIDMKGCIKVLKDQPPNSVEGLLNALRYTTKHLNDETTSKQIKSMLQ
          TSKIDMKGCIKVLKDQPPNSVEGLLNALRYTTKHLNDETTSKQIKSMLQ
Retrocopy TSKIDMKGCIKVLKDQPPNSVEGLLNALRYTTKHLNDETTSKQIKSMLQ

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	0.33 RPM	40.45 RPM
SRP017611_kidney	0.41 RPM	7.50 RPM
SRP017611_liver	0.00 RPM	4.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_953 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_953 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953 ,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978,