RetrogeneDB ID: retro_ocun_1682

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018762:1172204..1172791(+)
• 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_1682
GATTTAATTTATTGTGGTGATAGAGTCCAGAAAGGCCATGAAAACTATGTGAAAATTTTACTGAATGTGGGAGGCATGCT
AGTCATGCCTATAGAAGATCAGCTAACACAGATTATGTGACTGGGACAAAACATTTGGGAAAGTAAAAATATCCTTTTTG
TTTCATTTGCTCCACTTGTGCAGCCAAGTAAGAATGGTTATGGCAAGCCTGCTTCTGTGGGACTCCCCCCTGTGCTGTCA
GGAACCTGCAGGACTTGGCCTGTATTTACATTCACCGCCCACTTAGAAATTTCATAAACAATGAGACGCAGGCCAAAGGG
TTTTCCCAAAATATTCCACCCAAAAGGAAAAGAGAGTGAAAGAGAGTGAAACAGAATTAACAGGCACATCCTTGTAGGTA
ATCAGCTTATGCCTCAGCCTCTGGACAGTAAGGAGGATGAGAAAATGGAAGATCCCAAAGAAGAGGAGAAAGACCACAGT
GAAGCCATGAAGCCAGAAGAGCTGCCTCAGAATTCACAGAGAGAGAAAATCATGAAGCTGTCCTCCCTGAGACTTTAAAA
GCTTGCTTGAGATATTTTACAGACAAA

Alignment

ORF - retro_ocun_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 55.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DRIYCGAGVQKDHENYMKILLKVGGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLVQPSKNDNGKP
          D.IYCG..VQK.HENY.KILL.VGG.LVMPIEDQLTQIM..GQN.WESKNIL.VSFAPLVQPSKN..GKP
Retrocopy DLIYCGDRVQKGHENYVKILLNVGGMLVMPIEDQLTQIM*LGQNIWESKNILFVSFAPLVQPSKNGYGKP

Parental  DSVGLPP-CAVRNLQDLARIYIRRTLRNFINDEMQAKGIPQRAP-PKRKR-KRVKQRINTYVFVGNQLIP
          .SVGLPP.CAVRNLQDLA.IYI.R.LRNFIN.E.QAKG..Q..P.PK.K...R...RIN....VGNQL.P
Retrocopy ASVGLPP<CAVRNLQDLACIYIHRPLRNFINNETQAKGFSQNIP>PKGKESERE*NRINRHILVGNQLMP

Parental  QPLDSEEDEKMEEDHKEEEEREHSEAMKPEEPPQNLLREKIMKLP-LPESLKAYLTYFRDK
          QPLDS.EDEKME.....EEE..HSEAMKPEE.PQN..REKIMKL..LPE.LKA.L.YF.DK
Retrocopy QPLDSKEDEKMED--PKEEEKDHSEAMKPEELPQNSQREKIMKLS<LPETLKACLRYFTDK

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_1682 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1682 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 ,