RetrogeneDB ID: retro_ocun_536

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:135645846..135646883(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL15
• Ensembl ID: ENSOCUG00000014291
• Aliases: None
• Description: methyltransferase like 15 [Source:HGNC Symbol;Acc:26606]

Sequence

>retro_ocun_536
ATGCTTCGGTACTCATATTTTTGTAGAATATGTAAAGAATTTCCTTCATGCTGGTTGGAATTTGGCATGCTTAATTTAGT
TTTCTGTCCAAAAAAATACACAATACAGCAGAAGTACATAATGACTATGAAGCCCAGGGACAATCAGATCAAGCTCAGGA
GTTGCACAAATCTCAAAATAGAGATTCTAAAGCTATGACTGAATTACAGATTCCAGTAATGGTGGATGAAGTTGTCCGTT
GTTTGGCACCACAGAAAGAGCAGGTTTATCTATATATGACATTTGGTTCAGGAGGACACTCAAGAGCCATACTACAGAAA
GAGTCAGATATTACTCTATATGCCTTAGACAGAGACCCAACAGCTTACGCAATAGCTGAACAGCTTTCAGACTTATATCC
TAAACAAATCTGAGCCATGTTAGGCCAATTCAGCCAAGCAGAAGCCTTATTAATGAAAGCTGGAGTACAGCCAGGAACTT
TTGATGGAGTTCTTCTGGATCTTGGTTGTTCCTCCATGCGACTTGATGCTCCTGAAAGAGGTTTTTCCATTCAGAAGGAT
GGTCCATTAGACATGAGGATGGATGGTGGCAGGTACCCTGACATGCCCACCGCTGCTGATGTTGTGAATGCTTTAGATCA
ACAGGCACTTGCATCCATCCTCAGGACATACGGGGAGGAGAAGCACGCCAAGAAAATTGCTTCAGCAATCGTTCAGGCAC
GTAGCATCTACCCCATCACCAGAACCCAGCAGCTTGCCAGCATCGTTGCAGGTGCATTTCCTCCCTCTGCTATTTATGCA
CGAAAAGACATGCTACAGCGATCTACCCATATTGCTACCAAGACTTTCCAGGCTCTTCGCATATTTGTGAACAATGAGCT
CAATGAACTCTATACAGGACTAAAGACAGCACAGAAGTTGCTGAGACCTGGTGGATGACTTGTTGCCCTCTCTTTCCATT
CACTAGAAGATCACATAGTCAAACGATTTTTGCTTGGGATAAGCATGACGGAAAGGTTTAACTTAAGTGTTAGAAGG

Alignment

ORF - retro_ocun_536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.7 %
• Parental protein coverage: 85.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRYSYFCRICKEFPSCWLEFGMLNLGVWPKK-IHSTAEVHNDYEAQGQSDQTGAQELHKSQDRDSEAMT
          MLRYSYFCRICKEFPSCWLEFGMLNL...PKK.IH.TAEVHNDYEAQGQSDQ..AQELHKSQ.RDS.AMT
Retrocopy MLRYSYFCRICKEFPSCWLEFGMLNLVFCPKK<IHNTAEVHNDYEAQGQSDQ--AQELHKSQNRDSKAMT

Parental  ELHIPVMVDEVVRCLAPQKGQVFLDMTFGSGGHSRAILQKESDITLYALDRDPTAYAIAEQLSDLYPKQI
          EL.IPVMVDEVVRCLAPQK.QV.L.MTFGSGGHSRAILQKESDITLYALDRDPTAYAIAEQLSDLYPKQI
Retrocopy ELQIPVMVDEVVRCLAPQKEQVYLYMTFGSGGHSRAILQKESDITLYALDRDPTAYAIAEQLSDLYPKQI

Parental  RAMLGQFSQAEALLTKAGVQPGTFDGVLLDLGCSSMQLDAPERGFSIRKDGPLDMRMDGGRYPDMPTAAD
          .AMLGQFSQAEALL.KAGVQPGTFDGVLLDLGCSSM.LDAPERGFSI.KDGPLDMRMDGGRYPDMPTAAD
Retrocopy *AMLGQFSQAEALLMKAGVQPGTFDGVLLDLGCSSMRLDAPERGFSIQKDGPLDMRMDGGRYPDMPTAAD

Parental  VVNALDQQALASILRTYGEEKHAKKIASAIVQARSIYPITRTQQLASIVAGAFPPSAIYARKDLLQRSTH
          VVNALDQQALASILRTYGEEKHAKKIASAIVQARSIYPITRTQQLASIVAGAFPPSAIYARKD.LQRSTH
Retrocopy VVNALDQQALASILRTYGEEKHAKKIASAIVQARSIYPITRTQQLASIVAGAFPPSAIYARKDMLQRSTH

Parental  IATKTFQALRIFVNNELNELYTGLKTAQKFLRPGGRLVALSFHSLEDRIVKRFLLGISMTERFNLSVRQ
          IATKTFQALRIFVNNELNELYTGLKTAQK.LRPGG.LVALSFHSLED.IVKRFLLGISMTERFNLSVR.
Retrocopy IATKTFQALRIFVNNELNELYTGLKTAQKLLRPGG*LVALSFHSLEDHIVKRFLLGISMTERFNLSVRR

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	2.26 RPM
SRP017611_kidney	0.00 RPM	2.74 RPM
SRP017611_liver	0.00 RPM	2.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_536 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_536 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006142	2 retrocopies	retro_cjac_3301, retro_cjac_4047,
Homo sapiens	ENSG00000169519	2 retrocopies	retro_hsap_1123, retro_hsap_4656,
Macaca mulatta	ENSMMUG00000013616	1 retrocopy	retro_mmul_870,
Nomascus leucogenys	ENSNLEG00000017865	2 retrocopies	retro_nleu_1093, retro_nleu_187,
Oryctolagus cuniculus	ENSOCUG00000014291	1 retrocopy	retro_ocun_536 ,
Pongo abelii	ENSPPYG00000003399	1 retrocopy	retro_pabe_3617,
Pan troglodytes	ENSPTRG00000003461	1 retrocopy	retro_ptro_680,