RetrogeneDB ID: retro_ocun_417

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:4898753..4899747(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSOCUG00000013643
• Aliases: None
• Description: PDZ and LIM domain 1 [Source:HGNC Symbol;Acc:2067]

Sequence

>retro_ocun_417
GTTAGCACCCAGCAGATAGTCCCCCAGGACCCTGGACCATGGGGCTTCCCTCTCGTGGGCTGCAAGGACTTCCAGCAGCC
CCTCTCCGTTTCTCGGGTCACTCCCGCAAGCAGGGCTGCTTTAGCTAATTTATGAATCGGAGACGTAATCACAGCCATTG
ATGGGGAAAATACCAGCAGTATGACACATTTGGAAGCTCAGAACAAAATCAAGGGCTGCACGGACAACATTACTCTCACC
ATAGCAAGATCTGAACAGAAAATTTGGTCTCCTCTGGTGACGGAAGAGGGGAAACGTCACCCGTACAAGATGAATTTAGC
CTCAGAACCCCAGGAGGTCCTGCACTTAGGAAGCGTGCACAACCGAAGCGCCATGCCCAAACTTTACCGCCTCCCTGCTT
TGGTCACTGCCTCCAGAGTCATCACGAACCAGTACAACAACCCAGTCGGCCTCTACTCTTCGGAAAACATCTGCGCCTTC
CATAGTGCCTTGTAGGCAGGGAAGGCTACCAGCGGAGAGCAGGCCAACAGCAGACCCTTAGAACATTCACAGCTTCCAGG
CGGCCGCGTCATCGACAAGGAATCTGAAGTTTACAAGATGCTGCAGGAAAAAGCAGGAGTTGAATGAGCCCCTGAAGCAG
TCCACATCATTCTGGGTCCTGCAGGAAATCCTGGAGTCCGAGGAGAAAGGGGATCCCAACAAGCCCTCTGGATTCAGAAG
CGTTAGAGCTCCTGCCACCGAAGTAGCGGCATCGATTGGAAATGCTGCTCAGAAATTGCCCATGTGTGACAAATGTGCAC
TGGCATTGTAGGCGTGTTTGTGAAGCTGCAAGACCGTCACCGCCACCCCTGAGTGTTATGTGTGCTGCAACTGTGGCACC
AACCTGAAACAGAAGGGCCCCTTCCTTGTGGAGGATCAAATCTACTGTGAAAAGCACACCCGGGAGCGGGTCACGCCACC
TGAGGGCTAGAACGTGGTCACTGTATTTCCCAAG

Alignment

ORF - retro_ocun_417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSTQQIVLQGPGPWGFRLVGGKDFEQPLAVSRVTPGSKAALANLCIGDVITAIDGENTSSMTHLEAQNKI
          .STQQIV.Q.PGPWGF.LVG.KDF.QPL.VSRVTP.S.AALANL.IGDVITAIDGENTSSMTHLEAQNKI
Retrocopy VSTQQIVPQDPGPWGFPLVGCKDFQQPLSVSRVTPASRAALANL*IGDVITAIDGENTSSMTHLEAQNKI

Parental  KGCTDNITLTIARSEHKIWSPLVTEEGKRHPYKMNLASEPQEVLHIGSAHNRSAMP-FTASPASVTAPRV
          KGCTDNITLTIARSE.KIWSPLVTEEGKRHPYKMNLASEPQEVLH.GS.HNRSAMP.....PA.VTA.RV
Retrocopy KGCTDNITLTIARSEQKIWSPLVTEEGKRHPYKMNLASEPQEVLHLGSVHNRSAMPKLYRLPALVTASRV

Parental  ITNQYNNPVGLYSSENISTFNSALEARTATSGEEANSRPLEHSQPPGGLVIDKESEVYKMLQE-KQELNE
          ITNQYNNPVGLYSSENI..F.SAL.A..ATSGE.ANSRPLEHSQ.PGG.VIDKESEVYKMLQE.KQELNE
Retrocopy ITNQYNNPVGLYSSENICAFHSAL*AGKATSGEQANSRPLEHSQLPGGRVIDKESEVYKMLQE>KQELNE

Parental  PPKQSTSFRVLQEILESEEKGDPNKPSGFRSVKAPVTKVAASIGNAAQKLPMCDKCG-TGIVGVFVKLRD
          P.KQSTSF.VLQEILESEEKGDPNKPSGFRSV.AP.T.VAASIGNAAQKLPMCDKC..TGIVGVFVKL.D
Retrocopy PLKQSTSFWVLQEILESEEKGDPNKPSGFRSVRAPATEVAASIGNAAQKLPMCDKCA<TGIVGVFVKLQD

Parental  RHRH-PECYVCSDCGTNLKQKGHFFVEDQIYCEKHARERVTPPEGYDVVTVFPK
          RHRH.PECYVC..CGTNLKQKG.F.VEDQIYCEKH.RERVTPPEG..VVTVFPK
Retrocopy RHRH>PECYVCCNCGTNLKQKGPFLVEDQIYCEKHTRERVTPPEG*NVVTVFPK

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	1.71 RPM
SRP017611_kidney	0.00 RPM	13.78 RPM
SRP017611_liver	0.08 RPM	14.80 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_417 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_417 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_417 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417 ,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,