RetrogeneDB ID: retro_ocun_560

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:46227237..46228011(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023071
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KL
• Ensembl ID: ENSOCUG00000017687
• Aliases: KL, Kitl
• Description: klotho (KL), mRNA [Source:RefSeq mRNA;Acc:NM_001082223]

Sequence

>retro_ocun_560
ATTTATCTTCAACACTTCCCATTTAATCCTCTTGTCAAAACTAAGGCAATCTTTGGGAATCATGTGACTGATAATGTAAA
AGACATCACAAAATTGGTGGCAAATCTTCCAAAAGATTATATGATAACCCTCAACTATGTCCCCGGGATGGACATTTTGC
CAAGTCATTGTTGGATACATGAGATGGTAATACAGCTGTCAGTCAGCTTGACTAACCTTCTGGATAAGTTTTCAAATGTT
TCTGAAGGCTTGAGTAATTATTCTATCATAGACAAACTTGGGAAAATAGTGGATGACCTTGTGGAGTGCGTGGAAGAAAA
CTCACTAAGAATGTAAAAGTATCATCTGAGAGGTCCAAACCCAGGCCCTTTACTACTGAACAATTCTTTAGAATTTTTAA
TGGATCCATCGATGCCTTCAAGGACTTTATGGTGGTATCTGAAACTAGTGATTGGGTGGTTTCTTCATTATTAAGTTCTG
AGAAAGACTCCAGAGTCAGCGTCACAAAACCATTTATGTTATCCCGTTGCATCCCACTCCCTTAGGAATGACGGCTGTAG
CAGTAACAGCAAGGATGCAAGTTTCATTGGCGACTCCAGCCTACAATGGGCAGCCATGGCTTTGCCAGTATTCTTTTCTC
TTGTAATTGGTTTTGCTTTTGGAGCCTTATACTGGAAGAAGGAACAACCAAATCTTACAAGGACAGTTGAAAATATACAG
AGTAATGAAGAGGATAATGAGATAAGTATGTTGCAAAAAGAGTTTCAAGAAGTA

Alignment

ORF - retro_ocun_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.47 %
• Parental protein coverage: 95.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IYLQLLLFNPLVKTKGICGNLVTDNVKDITKLVANLPKDYMITLNYVPGMDILPSHCWIHEMVIQLSVSL
          IYLQ...FNPLVKTK.I.GN.VTDNVKDITKLVANLPKDYMITLNYVPGMDILPSHCWIHEMVIQLSVSL
Retrocopy IYLQHFPFNPLVKTKAIFGNHVTDNVKDITKLVANLPKDYMITLNYVPGMDILPSHCWIHEMVIQLSVSL

Parental  TNLLDKFSNISEGLSNYSIIDKLGKIVDDLVECVEENS-PKNVKASSKRPEPRPFTPEQFFRIFNRSIDA
          TNLLDKFSN.SEGLSNYSIIDKLGKIVDDLVECVEENS..KNVK.SS.R..PRPFT.EQFFRIFN.SIDA
Retrocopy TNLLDKFSNVSEGLSNYSIIDKLGKIVDDLVECVEENS<TKNVKVSSERSKPRPFTTEQFFRIFNGSIDA

Parental  FKDFVVVSETSDCVLPSTLSPEKDSRVSVTKPFML-PPVAASSLRNDSSSSNSKAESSIADSSLQWAAMA
          FKDF.VVSETSD.V..S.LS.EKDSRVSVTKPFML.P....S.LRND..SSNSK..S.I.DSSLQWAAMA
Retrocopy FKDFMVVSETSDWVVSSLLSSEKDSRVSVTKPFML>PVASHS-LRNDGCSSNSKDASFIGDSSLQWAAMA

Parental  LPAFFSLVIGFAFGALYWKKKQPNLTRAGENIQSNEEDNEISMLQEKEREFQEV
          LP.FFSLVIGFAFGALYWKK.QPNLTR..ENIQSNEEDNEISMLQ....EFQEV
Retrocopy LPVFFSLVIGFAFGALYWKKEQPNLTRTVENIQSNEEDNEISMLQ---KEFQEV

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	49.01 RPM
SRP017611_kidney	0.00 RPM	28.99 RPM
SRP017611_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_560 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019661	2 retrocopies	retro_cjac_3502, retro_cjac_3860,
Oryctolagus cuniculus	ENSOCUG00000017687	1 retrocopy	retro_ocun_560 ,
Otolemur garnettii	ENSOGAG00000009638	1 retrocopy	retro_ogar_2863,