RetrogeneDB ID: retro_ocun_565

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:72762838..72763928(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLDN
• Ensembl ID: ENSOCUG00000006860
• Aliases: None
• Description: gliomedin [Source:HGNC Symbol;Acc:29514]

Sequence

>retro_ocun_565
GCCACAGGAAATCCAGGGGAAAAGGGAGAGAGGGGGGACGTCGGTGAACTGGGCTCGACTGGCAACGAGGCCCCGCCGGG
GCAGAAGGGAGCCAAGGGAGATGCGTCCAATGATGTGCTTGTAGCAGGTGCCAAAGGTGACCCAGGCCCAGCCGGCCCAC
CTGGGCCCCCAGACCCCCCAGGGCCTCCAGGGCCCCCTGGAAGCAGAAGATCCAAAGGCCCTCAGCAGCCAAACCTGTTC
AATGGCCAGTGCCCAGGCGAGACATGTGCCATACCCAATGATGACACCTTGGTTGGAAAAGTTGATGAGAAAGTCAATGA
GCATCACTCCCCCAAAGCAGAATCAACGATCACCTCCATTGGGAACCCAACACAAGTCTTCAAGGTCAAGGAGAATTTTG
GGGCTTGGATACAAGAGTCTGCTATTAAGAACGACAGCTGCATCTGGGTGACTGAACACTTTTCAGGCATCATGGTGATG
GAATTCAAAGGCCAGACCGTCCTCCTGAACGGCAGCTGCACGATCATTCACCTCCTACTATTTCCATGGCTGCGGCCACA
CCTTGTACAACAACTCTCTCTACTACCACAAAGGGGGCTCCAACACCATCGTGAGATTCGATTTTGGCAAAGAAACATCT
GAAACGCTGAAGCTTAAAAACTCCCGGTATTTTGACTGCAAATACCTTTTCGTCAATTCCAAGACGTACTTCAACCTGGC
TATGGACGAACAGGAGCTGTGGGTCATCTACGCTTCGAGCGCGGATGGCTCGAGCTTCCTTGTTGTGCAGCTGGAGGAGA
GGACCTTCTCTGTGGCACAGCACATCAATACCACCTACCCAAAGTCCAAGGCAGGCAACGCCTTCATCGCCCACGGGATC
CTCTACGTCACAGACACCAAAGACACAAGGATAACGTTCGCCTTCGATCTGTTAGGAGGAAAGCAGATCAACGCCAGCTT
TGATGTCAGAACTTCCCAGTCTGTTCTGGCCATGTTAGCCTACAACATGAGAGACCAGCACCTGTACTCCTGGGAAGATG
GCCACCTGCTGCTGTACCCAGTGCAGTTCCTGGCGGCTCCGTTCAGCCAG

Alignment

ORF - retro_ocun_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AIGNPGEKGEKGDVGELGSTGNEGPPGQKGAKGDKGDASNDVLVA---GDPGPAGPPGPPGPPGPPGPPG
          A.GNPGEKGE.GDVGELGSTGNE.PPGQKGA...KGDASNDVLVA...GDPGPA...............G
Retrocopy ATGNPGEKGERGDVGELGSTGNEAPPGQKGA---KGDASNDVLVAGAKGDPGPAXXXXXXXXXXXXXXXG

Parental  SRRSKGPRQPNLFNGQCPGETCAIPNDDTLVGKVDEKVNEHHSPKAESTITSIGNPTQVFKVKETFGTWI
          SRRSKGP.QPNLFNGQCPGETCAIPNDDTLVGKVDEKVNEHHSPKAESTITSIGNPTQVFKVKE.FG.WI
Retrocopy SRRSKGPQQPNLFNGQCPGETCAIPNDDTLVGKVDEKVNEHHSPKAESTITSIGNPTQVFKVKENFGAWI

Parental  RESANKNDSRIWVTEHFSGIIVKEFKDQAALLNGSCTFIHLPYYFHGCGHTVYNNSL-YYHKGGSNTIVR
          .ESA.KNDS.IWVTEHFSGI.V.EFK.Q..LLNGSCT.IHL........H.V...SL.Y..KGGSNTIVR
Retrocopy QESAIKNDSCIWVTEHFSGIMVMEFKGQTVLLNGSCTIIHLLLFPWLRPHLVQQLSL>YH-KGGSNTIVR

Parental  FDFGKETSETLKLENALYFDRKYLFTNSKTYFNLAVDEQGLWIIYASSVDGSSILVAQLEERTFSVAQHI
          FDFGKETSETLKL.N..YFD.KYLF.NSKTYFNLA.DEQ.LW.IYASS.DGSS.LV.QLEERTFSVAQHI
Retrocopy FDFGKETSETLKLKNSRYFDCKYLFVNSKTYFNLAMDEQELWVIYASSADGSSFLVVQLEERTFSVAQHI

Parental  NTTYPKSKAGNAFIAHGILYVTDTKDTRVTFAFDLLGGKQINANFDVRTSQSVLAMLAYNMRDQHLYSWE
          NTTYPKSKAGNAFIAHGILYVTDTKDTR.TFAFDLLGGKQINA.FDVRTSQSVLAMLAYNMRDQHLYSWE
Retrocopy NTTYPKSKAGNAFIAHGILYVTDTKDTRITFAFDLLGGKQINASFDVRTSQSVLAMLAYNMRDQHLYSWE

Parental  DGHLLLYPVQFLAAPFSQ
          DGHLLLYPVQFLAAPFSQ
Retrocopy DGHLLLYPVQFLAAPFSQ

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	5.08 RPM
SRP017611_kidney	0.00 RPM	2.03 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_565 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_565 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000006860	1 retrocopy	retro_ocun_565 ,