RetrogeneDB ID: retro_ocun_824

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:26535175..26536500(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000002051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFAF7
• Ensembl ID: ENSOCUG00000007239
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 7 [Source:HGNC Symbol;Acc:28816]

Sequence

>retro_ocun_824
ATGAGTGTCCTGCTGCTGTCCGGCCGGGCTTGGCTGTGCTCTGCGGCGCGCGGGGTCTTTCCCTGTCTTTGGAGAGGGAA
ATGCTTCGGCACTGGGAATGAGCGGGCAGAAAAGAACCCGACGACGCCGATGCTGCGGCATCTGGTGTATAAAATAAAGT
CCACTGGCCCCATCACTGTGGCCGAGTACATGAAGGAGGTGTTGACCAATCCAGCCAAGGGATATTATGTGTACCGTGAC
ATGCTGGGAGAAAAAGGAGATTTCGTTACTTCACCTGAAATAAGTCAGATCTTTGGGGAGCTGCTAGGGATATGGTTCAT
TAGTGAGTGGATGGCCACTGGAAAAAGTGCAGCTTTCCAGCTGGTGGAACTGGGCCCTGGTAGGGGAACCCTCGCAGGGG
ATATTTTGAGGGTGTTTAGTCAGCTTGGATCTGTGCTGAAAAACTGTGACATTTCCATACATCTGGTGGAGGTGAGCCAA
AAACTAAGTGAGATTCAAGCAGTGACGCTGACTGAAGAGAAGGTCCCGTTAGAGCGGAATGCTGACTCCCCAGTGTATAT
GAAAGGTGTTTCTAAGACTGGGATTCCAGTTTGCTGGTACCGAAATCTGCAAGATGTCCCAAAAGGATACAGCTTTTATC
TTGCACATGAATTCTTCGATGTTCTTCCTGTGCATAAGTTTCAGAAAACACCACAAGGATGGCGAGAAGTGCTCATCGAT
ATTGATCGGCAAGTTTCTGATAAACTGAGGTTTGTCTTGGCGCCTTGTGCACTCCAGCAGAAGCCTTCATACACCACGAT
GAAAAAAGGGATCACGTTGAAGTGTGTCCCGACGCCGGTGTCGTCATTCAGGAACTTTCTCAACGTATTGCACTGACTGG
AGGTGCTGCGCTGATTGCTGATTACGGCCATGATGGAACAAAGACAGATACCTTCAGAGGATTCTGTGGCCACAAGCTGC
ATGATGTGTTGGTCGCCCCAGGAATGGCAGACCTAACAGCTGACGTGGACTTCAGTTACCTGCGCAGAATGGCACAAGGA
CAAGTAGCCTCGCTGGGCCCAATAACACAACAAACATTTTTAAAAAATATGGGCATTGATGTTCGGCTGAAGATTCTTGC
AGATAAATCACATGAGCCTTCAGTTAGGCAACAGTTACTTCAGGGATATGATATGCTCATGAACCCTAAGAAGATGGGAG
AAAGATTTCACTTTTTTGCACTGCTGCCTCATCAGAGACTCCGTGGTGGAAGTCACCAGACAGAAGCACGGCCGTCAAGA
CCCTCTGTGGCGCCTGTGGCTGGCTTTGCTGACCTTGCTTGGAGG

Alignment

ORF - retro_ocun_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVLLLSGRAWLCSAARGVFPCLWRGKCFCTGNERAEKNPTTPMLRHLVYKIKSTGPITVAEYMKEVLTN
          MSVLLLSGRAWLCSAARGVFPCLWRGKCF.TGNERAEKNPTTPMLRHLVYKIKSTGPITVAEYMKEVLTN
Retrocopy MSVLLLSGRAWLCSAARGVFPCLWRGKCFGTGNERAEKNPTTPMLRHLVYKIKSTGPITVAEYMKEVLTN

Parental  PAKGYYVYRDMLGEKGDFVTSPEISQIFGELLGIWFISEWMATGKSAAFQLVELGPGRGTLAGDILRVFN
          PAKGYYVYRDMLGEKGDFVTSPEISQIFGELLGIWFISEWMATGKSAAFQLVELGPGRGTLAGDILRVF.
Retrocopy PAKGYYVYRDMLGEKGDFVTSPEISQIFGELLGIWFISEWMATGKSAAFQLVELGPGRGTLAGDILRVFS

Parental  QLGSVLKNCDISIHLVEVSQKLSEIQAVTLTEEKVPLERNADSPVYMKGVSKTGIPVCWYRNLQDVPKGY
          QLGSVLKNCDISIHLVEVSQKLSEIQAVTLTEEKVPLERNADSPVYMKGVSKTGIPVCWYRNLQDVPKGY
Retrocopy QLGSVLKNCDISIHLVEVSQKLSEIQAVTLTEEKVPLERNADSPVYMKGVSKTGIPVCWYRNLQDVPKGY

Parental  SFYLAHEFFDVLPVHKFQKTPQGWREVLIDTDPQVSDKLRFVLAPCA-TPAEAFIHHDEKRDHVEVCPDA
          SFYLAHEFFDVLPVHKFQKTPQGWREVLID.D.QVSDKLRFVLAPCA.TPAEAFIHHDEKRDHVEVCPDA
Retrocopy SFYLAHEFFDVLPVHKFQKTPQGWREVLIDIDRQVSDKLRFVLAPCA<TPAEAFIHHDEKRDHVEVCPDA

Parental  GVVIQELSQRIALTGGAALIADYGHDGTKTDTFRGFCGHKLHDVLIAPGMADLTADVDFSYLRRMAQGQV
          GVVIQELSQRIALTGGAALIADYGHDGTKTDTFRGFCGHKLHDVL.APGMADLTADVDFSYLRRMAQGQV
Retrocopy GVVIQELSQRIALTGGAALIADYGHDGTKTDTFRGFCGHKLHDVLVAPGMADLTADVDFSYLRRMAQGQV

Parental  ASLGPITQQTFLKNMGIDVRLKILADKSHEPSVREQLLQGYDMLMNPKKMGERFHFFALLPHQRLRGGSH
          ASLGPITQQTFLKNMGIDVRLKILADKSHEPSVR.QLLQGYDMLMNPKKMGERFHFFALLPHQRLRGGSH
Retrocopy ASLGPITQQTFLKNMGIDVRLKILADKSHEPSVRQQLLQGYDMLMNPKKMGERFHFFALLPHQRLRGGSH

Parental  QTEARPSRPSVAPVAGFADLAWR
          QTEARPSRPSVAPVAGFADLAWR
Retrocopy QTEARPSRPSVAPVAGFADLAWR

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	1.99 RPM	7.34 RPM
SRP017611_kidney	2.13 RPM	8.11 RPM
SRP017611_liver	0.85 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_824 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_824 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000007239	1 retrocopy	retro_ocun_824 ,
Otolemur garnettii	ENSOGAG00000002568	1 retrocopy	retro_ogar_1105,
Rattus norvegicus	ENSRNOG00000005279	1 retrocopy	retro_rnor_1231,