RetrogeneDB ID: retro_ocun_1920

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:27337503..27338476(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001445
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MFAP3L
• Ensembl ID: ENSOCUG00000011514
• Aliases: None
• Description: microfibrillar-associated protein 3-like [Source:HGNC Symbol;Acc:29083]

Sequence

>retro_ocun_1920
CATCTGAAAGTGTGCTGTCTACATTCTGTGCCCTTTTTAATCCTAGTATCCACTCTAGCCACTGCTGGAGTGTGACGAAC
AGCACTTTAAATGGCACTGACATGGTCTTGGGCTCCGTGCCCACAATCACAGCCAGAACTGACCACATCATAGTCAAGGA
AGAGAACAGTGCCTTGATTCACTGTAGTGTTTGTGGCATCCCTGACCCGCAGTTCAAGTGGTATAAGTGCATGGGCAAGC
TGCTGAAAGAAGAAAAGAAGGAAAGAGGAGGAGGGAAATGGCCAGTGCATGACAGTGGGCTCCTGAGCATCACCAAGGCA
TCTTTCTCAGATGGAGGTAAATACACGTGTGTGGTTTCCAACATCTATGGCAGTGTGAACAACACAGTGACCCTGAGAGC
CATCTTTACCTCTGGAGACATGGGCGTCCACTACATGGTTGTCTGCCTTGTGGCCTTCACCATTATCATGGTCCTCAACA
TCACCCGCCTGTGCATGATGAGCAGCCACCTGAAGAAGACTGAGAAAGCCATCAACCAGTTCTTTAGGACAGAAGGCGCA
GAGCAGCTGCAGAAGGCATTTGAGATCGCCAAGTGGATCCCCATCATCACCTCAGCCAAAACTCTATAGAGTTTGCCAAA
GTCACCCAGTTCAAAACCATGGAGTTTGCCCGCTATATTGAAAAGCCTGCCAGGAGTGCGCCTCTACCTCCTCTCATTGT
GAACTGCAGGACGATCATGGAGATCATGGAAGTGGTGAGGCTGGAGGAGCAGGGGCAGAACTTTGTGAGGCATACTCCCG
AAGGCCGGGAGGCTGCAGACAGGGGTGAGGTCTACACGATCCCCAACTCTCTGAAGCGAAGTGACTCTCCCACCGCCAAC
TCAGATGCCTCGTCCCTGCACGAACAGCCTCAGCAGATGGCCATTAAGGTGCCCATTCACCCACAGTCCAAAAAGGATCA
CGTGGACGAGCAG

Alignment

ORF - retro_ocun_1920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.89 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HLFILILNQVPALWIQVSTLATAR-SVTNSTLNGTDMVLGSVPVIMARTDHIIVKEGNSALINCSVYGVP
          HL....L..VP.L.I.VSTLATA..SVTNSTLNGTDMVLGSVP.I.ARTDHIIVKE.NSALI.CSV.G.P
Retrocopy HLKVCCLHSVPFL-ILVSTLATAG<SVTNSTLNGTDMVLGSVPTITARTDHIIVKEENSALIHCSVCGIP

Parental  DPQFKWYNSMGKLLKEEEDEKERGGGKWQMHDSGLLNITKVSFSDRGRYTCVASNIYGSVNNTVTLRVIF
          DPQFKWY..MGKLLKEE...KERGGGKW..HDSGLL.ITK.SFSD.G.YTCV.SNIYGSVNNTVTLR.IF
Retrocopy DPQFKWYKCMGKLLKEEK--KERGGGKWPVHDSGLLSITKASFSDGGKYTCVVSNIYGSVNNTVTLRAIF

Parental  TSGDMGVYYMVVCLVAFTIVMVLNITRLCMMSSHLKKTEKAINEFFRTEGAEKLQKAFEIAKRIPIITSA
          TSGDMGV.YMVVCLVAFTI.MVLNITRLCMMSSHLKKTEKAIN.FFRTEGAE.LQKAFEIAK.IPIITSA
Retrocopy TSGDMGVHYMVVCLVAFTIIMVLNITRLCMMSSHLKKTEKAINQFFRTEGAEQLQKAFEIAKWIPIITSA

Parental  KTL-ELAK-VTQFKTMEFARYIEELARSVPLPPLIMNCRTIMEEIMEVVGLEEQGQNFVRHTPEGQEAAD
          KTL..L.K.VTQFKTMEFARYIE..ARS.PLPPLI.NCRTIM.EIMEVV.LEEQGQNFVRHTPEG.EAAD
Retrocopy KTL*SLPK<VTQFKTMEFARYIEKPARSAPLPPLIVNCRTIM-EIMEVVRLEEQGQNFVRHTPEGREAAD

Parental  RDEVYTIPNSLKRSDSPTADSDASSLHEQPQQIAIKVSIHPQSKKDHVDEQ
          R.EVYTIPNSLKRSDSPTA.SDASSLHEQPQQ.AIKV.IHPQSKKDHVDEQ
Retrocopy RGEVYTIPNSLKRSDSPTANSDASSLHEQPQQMAIKVPIHPQSKKDHVDEQ

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	15.29 RPM
SRP017611_kidney	0.00 RPM	62.33 RPM
SRP017611_liver	0.00 RPM	11.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1920 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1920 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	ENSOCUG00000011514	1 retrocopy	retro_ocun_1920 ,