RetrogeneDB ID: retro_ocun_1552

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018699:9342405..9343187(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000017167
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CALB1
• Ensembl ID: ENSOCUG00000006341
• Aliases: None
• Description: calbindin 1, 28kDa [Source:HGNC Symbol;Acc:1434]

Sequence

>retro_ocun_1552
ATTGCAGAATCCCACCTGCAATCATCCCTGATCACAGCCTCACAGTTTTTCGAGATCTGGCTTCATTAGGACGCTGATGG
AAGTGGTTACCTGGAGGGAATGGAGCTGCAGAACTTGATCCAGGAGCTCCAGCAGGTGCGAAAGAAGGCTGGGTTGGAAT
TATCACCTGAGATGAAAACTTTTGTGGATCAGTATGGGCAGAGAGATGATGGAAAAAAAGGAATTGTAGAGTTGGCCCAT
GTATTACCCACAGAAGAGAATTTCTTGCTGCTCTTCCGGTGCCAGCAGCTGAAGTCCTGTGAGGAATTCATGAAGACATG
GAGAAAATGTGATACTGAACACAGTGGCTTCATAGAAACTGAGGAACTTAAGAACTTTCTAAAGGATCTGCTGGAAAAAG
CAAACAAGACGGTAGATGACACAAAATTAGCTGAGTATACAGACCTAATGCTGAAACTATTTGATTCAAATAATCATGGG
AAGCTGGAATTAACTGAGATGGCCAGGTTATCACCAGTGCAAGAGAATTTTCTTCTTAACTTTCAGGGAATCAAAATGTG
TGGGAAAGAGTTCAATAAGGCTTTGAGTTATAAGATCAGGATGGTAACGGGTACATAGATGAAAATGAACTGGATGCCTT
ACTGAAGGATCTGTGTGAGAAGAATAAACAGGAACTGGATATTAATAATATTCCAACATACAAGAAGAGCATAATGGCTT
TGTCGGATTGAGGGAAGCTCTACGGAACAGATCTTGCTCTTATTCTTTGTGCTGGATACAAC

Alignment

ORF - retro_ocun_1552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAESHLQSSLITASQFFEIWLHYDADGSGYLEGMELQNLIQELQQARKKAGLELSPEMKTFVDQYGQRDD
          .AESHLQSSLITASQFFEIWLH.DADGSGYLEGMELQNLIQELQQ.RKKAGLELSPEMKTFVDQYGQRDD
Retrocopy IAESHLQSSLITASQFFEIWLH*DADGSGYLEGMELQNLIQELQQVRKKAGLELSPEMKTFVDQYGQRDD

Parental  GKIGIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRKYDTDHSGFIETEELKNFLKDLLEKANKTVDD
          GK.GIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRK.DT.HSGFIETEELKNFLKDLLEKANKTVDD
Retrocopy GKKGIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRKCDTEHSGFIETEELKNFLKDLLEKANKTVDD

Parental  TKLAEYTDLMLKLFDSNNDGKLELTEMARRLLPVQENFLLKFQGIKMCGKEFNKA-FELYDQDGNGYIDE
          TKLAEYTDLMLKLFDSNN.GKLELTEMA.RL.PVQENFLL.FQGIKMCGKEFNKA.FEL.DQDGNGYIDE
Retrocopy TKLAEYTDLMLKLFDSNNHGKLELTEMA-RLSPVQENFLLNFQGIKMCGKEFNKA<FEL*DQDGNGYIDE

Parental  NELDALLKDLCEKNKQELDINNIPTYKKSIMALSDGGKLYRTDLALILCAGDN
          NELDALLKDLCEKNKQELDINNIPTYKKSIMALSD.GKLY.TDLALILCAG.N
Retrocopy NELDALLKDLCEKNKQELDINNIPTYKKSIMALSD*GKLYGTDLALILCAGYN

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	4.86 RPM	278.70 RPM
SRP017611_kidney	8.62 RPM	454.38 RPM
SRP017611_liver	0.00 RPM	0.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1552 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1552 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000006341	1 retrocopy	retro_ocun_1552 ,
Tupaia belangeri	ENSTBEG00000005714	1 retrocopy	retro_tbel_4715,