RetrogeneDB ID: retro_ocun_652

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:63970043..63971344(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008259
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSOCUG00000026311
• Aliases: None
• Description: matrin 3 (MATR3), mRNA [Source:RefSeq mRNA;Acc:NM_001205257]

Sequence

>retro_ocun_652
TACAAACTGCTACAGCTGGTGGAACCATTTGGAGTCATTTCAAATCATCTGATTCTAAATAAAATTAATGAGGCGTTTAT
TGAAATGGCAACCACAGAAGATGCTCAGGCTGCAGTGGACTATTATACAACCACACCAGCATTCGTATTTGGCAAGCCAG
TTAGAGCTTATTTGTCCCAGAAGTACAAAAGAATAAAGAAACCTGAGGGAAAGCCGCATCAGAAATTTGACCAAAAGCAA
GAGCTTGGCCGTGTGATACACCTCAGCAATTTGCCCCATTCTGACTGTTCTGATAGTGCTGTGCTCAAGCTTGCTGAACC
TTATGGAAAAATAAAGAATTACATACTGCTGAGGATGAAAAGTCAGGCCTTCATAGAGATGGAAACCAGAGAAGATGCGG
TGGCAATGGTTGACCATTGTTTGAAAAAGGCCCTTTGGTTCCAAGGGAGGTGTGTGAAGGCTGACCTGTCTGAGAAATAT
AAAAAACTGGTACTGAGGATTCCCAACAGAGGCACTGACTTACTGAAAAAGGATAAGTCTCAAAAAAGATCTTACTCTCC
AGATGGCAAGAATCTCCAAGTGATAAGAAATCCAAAACAGATGGCTCTCAGAAGACTGGAAGTACAACCGAAGGTAAAGA
ACAAGAAGAGAAGTCAGGTGAAGATGGAGAGAAAGATACAAAGGATGACCAGACAGAGCAGGAACCTAATGTGCTTCTTG
AATCTGAAGATGGACTACTTGTAGATGAAGCAGCAGCGGCAGCTCTACTAGAAAGTGGCAGTTCAGTGGGAGATGAGACC
GATCTTGCTAACTTAGGTGACGTTGCTTCTGATGGGATAAAGGAACCTTCAGACAAAGCTGTGAAAAAAGATACAAGTGC
TTCAACGGCAGCAAAGACAAAGCTTAAAAAGGTGGACAAGATCGAAAAACTTGATCAAGAAAATGAAGCAGCGTTGGAAA
ATGGAATTAAAAATGAGGAAAATGCAGAACCAGGTGCTGAATCTGCTGAGAATGCTGACGATCCCAGCAAAGACACAAGT
GAAAATGCAGATGGCCAAAGTGATGAAAACAAGGACTATACAATCCCAGATGAGTACAGAATTGGACCATATCAGCCCAA
TGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGCTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAG
AAATTGCAAAGAATACTCATTGTAACAGTCTTCCTCATTATCAGAAATTAAAGCAATTTCTGAATAAATTGGCAGAAGAA
TGCCGGCAGAAGAAGGAAGCT

Alignment

ORF - retro_ocun_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 51.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEG
          Y.LLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPA.VFGKPVR..LSQKYKRIKKPEG
Retrocopy YKLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPAFVFGKPVRAYLSQKYKRIKKPEG

Parental  KPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHC
          KP.QKFDQKQELGRVIHLSNLPHS..SDSAVLKLAEPYGKIKNYIL.RMKSQAFIEMETREDA.AMVDHC
Retrocopy KPHQKFDQKQELGRVIHLSNLPHSDCSDSAVLKLAEPYGKIKNYILLRMKSQAFIEMETREDAVAMVDHC

Parental  LKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGK-ESPSDKKSKTDGSQKTEST
          LKKALWFQGRCVK.DLSEKYKKLVLRIPNRG.DLLKKDKS.KRSYSPDGK.ESPSDKKSKTDGSQKT.ST
Retrocopy LKKALWFQGRCVKADLSEKYKKLVLRIPNRGTDLLKKDKSQKRSYSPDGK<ESPSDKKSKTDGSQKTGST

Parental  TEGKEQEEKSGEDGEKDTKDDQTEQEPNMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVASDG
          TEGKEQEEKSGEDGEKDTKDDQTEQEPN.LLESED.LLVDE..AAALLESGSSVGDETDLANLGDVASDG
Retrocopy TEGKEQEEKSGEDGEKDTKDDQTEQEPNVLLESEDGLLVDEAAAAALLESGSSVGDETDLANLGDVASDG

Parental  KKEPSDKAVKKDTSASTAAKKKLKKVDKIEELDQENEAALENGIKNEENAEPGAESAENADDPSKDTSEN
          .KEPSDKAVKKDTSASTAAK.KLKKVDKIE.LDQENEAALENGIKNEENAEPGAESAENADDPSKDTSEN
Retrocopy IKEPSDKAVKKDTSASTAAKTKLKKVDKIEKLDQENEAALENGIKNEENAEPGAESAENADDPSKDTSEN

Parental  ADGQSDENKEDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLK
          ADGQSDENK.DYTIPDEYRIGPYQPNVPVGIDYVIPKTG.YCKLCSLFYTNEE.AKNTHC.SLPHYQKLK
Retrocopy ADGQSDENK-DYTIPDEYRIGPYQPNVPVGIDYVIPKTGLYCKLCSLFYTNEEIAKNTHCNSLPHYQKLK

Parental  KFLNKLAEERRQKKEA
          .FLNKLAEE.RQKKEA
Retrocopy QFLNKLAEECRQKKEA

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	0.39 RPM	991.40 RPM
SRP017611_kidney	0.10 RPM	261.70 RPM
SRP017611_liver	0.08 RPM	110.99 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_652 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652 ,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,