RetrogeneDB ID: retro_ocun_1571

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018701:174893..175572(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCMTD1
• Ensembl ID: ENSOCUG00000016958
• Aliases: None
• Description: protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 [Source:HGNC Symbol;Acc:30483]

Sequence

>retro_ocun_1571
TTTGGGAAAAATCGTGGGATGCAGCTTCATTCAGATGTGGTAGACTATGCCAAGGAAAAACTGGAGAACTTCATCAAAAA
TAGTAGTAGCTTTGATGAATTTGAGTTCTGTGAACCTGCATTTGTGGTTGGTAATTGACTCCAGAGATCGTCTGAAAGTC
ATCCTTATGATCGTATTTATTGTGGTGCTGGAGTCCAGAAAGACCATGAAAACTACATGAACGTTTTACTGAACATGGGA
GCGTACCAGTCATGCTTATAGAAAATCAGTTAACACAGATTATGTTAACTGGAAAAATCACTTGGGAAAGTAAAAATATC
CTTGCTGTTTCATTTGCTCCACTGGTGCACCCAAGTGAGAATGATTATGGCACGCTTGCCTCTGTGGGACTGCCTCCTTG
ACCTGTCAGGAGCCTTCAGACTTATCCTGTATTTACATTCGCTGCACACTTAGAACTTTCATAAATGATGAGATGCAGGC
CCAAGGGATTTCCCAAAAGGCTCCACCCAAAAGGAAAAGAGAGTGAAACAGAATTAATAGGCACATCCTTGTAGGTAATC
AGCCTATTCCTCAACCTCTAGACAGTGAGGAGGATGAGAAAATGCAAGATCACAAAGAGGAGACAGACCAGAGTGAAGAC
ATGGAGCCAGAAGAGCCTCCTCAGAATCCACTGAGGGAG

Alignment

ORF - retro_ocun_1571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 64.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FGINHGIELHSDVVEYAKEKLESFIKNSDSFDKFEFCEPAFVVGNCLQIASDSHQYDRIYCGAGVQKDHE
          FG.N.G..LHSDVV.YAKEKLE.FIKNS.SFD.FEFCEPAFVVGN.LQ..S.SH.YDRIYCGAGVQKDHE
Retrocopy FGKNRGMQLHSDVVDYAKEKLENFIKNSSSFDEFEFCEPAFVVGN*LQRSSESHPYDRIYCGAGVQKDHE

Parental  NYMKILLKV-GGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLVQPSKNDNGKPDSVGLPPCAVRNL
          NYM..LL...G...VM.IE.QLTQIM.TG..TWESKNILAVSFAPLV.PS.ND.G...SVGLPP..VR.L
Retrocopy NYMNVLLNM<GSVPVMLIENQLTQIMLTGKITWESKNILAVSFAPLVHPSENDYGTLASVGLPP*PVRSL

Parental  Q-DLARIYIRRTLRNFINDEMQAKGIPQRAPPKRKRKRVKQRINTYVFVGNQLIPQPLDSEEDEKMEEDH
          Q.DL..IYIR.TLR.FINDEMQA.GI.Q.APPKRKR.....RIN....VGNQ.IPQPLDSEEDEKM..DH
Retrocopy Q<DLSCIYIRCTLRTFINDEMQAQGISQKAPPKRKRE--*NRINRHILVGNQPIPQPLDSEEDEKM-QDH

Parental  KEEEEREHSEAMKPEEPPQNLLRE
          KEE.....SE.M.PEEPPQN.LRE
Retrocopy KEETDQ--SEDMEPEEPPQNPLRE

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	0.00 RPM	90.95 RPM
SRP017611_kidney	0.00 RPM	142.00 RPM
SRP017611_liver	0.00 RPM	131.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1571 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1571 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
Cavia porcellus	ENSCPOG00000006593	1 retrocopy	retro_cpor_63,
Monodelphis domestica	ENSMODG00000009645	1 retrocopy	retro_mdom_640,
Oryctolagus cuniculus	ENSOCUG00000016958	2 retrocopies	retro_ocun_1571 , retro_ocun_1682,