RetrogeneDB ID: retro_ocun_1528

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02076170:121144..122545(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026453
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSOCUG00000001272
• Aliases: None
• Description: major facilitator superfamily domain containing 1 [Source:HGNC Symbol;Acc:25874]

Sequence

>retro_ocun_1528
TCGGAGTCTCCCACGAGGCCGTGGATTAGGAGGATGAGGAAGCAAGGGCGCTGCTGGTGGGCGGCACCGATGAGGCCAAC
CCAGGGGCCCCCGCTGCCTCATGGGCACTGCCAGCCCTCTGCGACCCCAGTCACCTGGTGCACTGGCTTTTGGTGCTGCT
GCCAATGTGCTTCCTGGGCTTTGGCAGTTATTTTTGCTATGATAATCCTGCTGCCCTTCAGACTCAGATTAAACAGGATA
TGCAGGTGAATACCACGAAATCCATGCGGCTGTATATCTGGTATTCTTGGTTTTGTGTTTCTTTGGTGGCTTTTTGATAG
ACCGAGTATTTGGAATATGGTGGGGCACAATAATTTTTAGCTGCTTTGTTTGCATTGGACAGGTTATCTTTGCTCTGGGG
GGAATATTTAATGCTTTTTGGCTGATGGAATTTGGAAGGTTTGTGTTTAGGATTGGTGGGAAGTCTTTAGCTGTTGCCCA
GAATACATATGCTGTAAATTGGTTTAAAGGCAAAGAACTAAACCTGGTGTTTGGGCTCCAACTTAGCATGGCTAGAATTG
GCAGCACAGTAAACATGAACCTCATGGGCTGGCTGTATTCTAAGGTTGAAGCTTCATTGGGTTCTGCTGGTCATACAACC
CTTGGGGTGACACTTATGATTGGAGGCTTAACGTGTGTTCTTTCCCTAATCTGTGCCTTGGTCCTTGCCTATTTGGATCA
GAGAGCAGAGAGAATCCTTCATAAAGAGCAAGGGAAAACAGGGGAGGTTATCAAATTAACAAATGTGAAGGACTTCTCCT
TGCCGCTGTGGCTCATCTTTGTCATCTGTGTCTGCTATTATGTCGTGGTCTTCCCTTTCACTGGACTTGGAAAAGTTTTC
TTTACAGAGAAATTTGGATTTTCTTCCCAGGCCGGAAGAGCAATTAACAGTATCGTGTATGTCATATCAGCACCCATGTC
TCCAGTGTTCGGGCTCCTAGTGGATAAAACAGGCAAGAACATCATCTGGGTCCTGTGTGCGGTAGCAGCTGCTCTGTGTC
CCACATGAAGCTGGCCTTCACGATGTGGAACCCGTGGATTGCCATGTGCCTGCTGGGACTGTCGTATTCGCTGCTGGCCT
GTGCGCTGTGGCCCATGGTGGCGTTTGTAGTTCCTGAGCATCAGCTGGGAACTGCATATGGCTTCATGCAGTCCATTCAG
AATCTCGGGCTGGCGGTCATCTCCATCATTGCTGGCATGATACTGGATACTCAGGGATACTTGTTTTTAGTTTACTTCAT
AGCCTGTGTTTCTTTGTCACTTTTATCTGTGGTCTTACTCTATTTCGTGGATCATGCCCGAGGAGGGAATCTAAATTATT
CTGCAAGACAAAGGGAAGAAATGAAAATGTCCCATACTGAA

Alignment

ORF - retro_ocun_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.37 %
• Parental protein coverage: 92.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRSPARP-MDEEDEEARALLAGGADEADPGAPAASRALPALCDPSRLAHRLLVLLLMCFLGFGSYFCYDN
          S.SP.RP..D.EDEEARALL.GG.DEA.PGAPAAS.ALPALCDPS.L.H.LLVLL.MCFLGFGSYFCYDN
Retrocopy SESPTRP<VD*EDEEARALLVGGTDEANPGAPAASWALPALCDPSHLVHWLLVLLPMCFLGFGSYFCYDN

Parental  PAALQTQVKQDMQVNTTKFMLLYAWYSWPN-VVLCFFGGFLIDRVFGIRWGTIIFSCFVCIGQVIFALGG
          PAALQTQ.KQDMQVNTTK.M.L...Y.W....VLCFFGGFLIDRVFGI.WGTIIFSCFVCIGQVIFALGG
Retrocopy PAALQTQIKQDMQVNTTKSMRL---YIWYS<LVLCFFGGFLIDRVFGIWWGTIIFSCFVCIGQVIFALGG

Parental  IFNAFWLMEFGRFVFGIGGESLAVAQNTYAVSWFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKVEA
          IFNAFWLMEFGRFVF.IGG.SLAVAQNTYAV.WFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKVEA
Retrocopy IFNAFWLMEFGRFVFRIGGKSLAVAQNTYAVNWFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKVEA

Parental  SLGSAGHTTLGVTLMIGGLTCVLSLICALALAYLDQRAERILHKEQGKTGEVIKLTDVKDFSLPLWLIFV
          SLGSAGHTTLGVTLMIGGLTCVLSLICAL.LAYLDQRAERILHKEQGKTGEVIKLT.VKDFSLPLWLIFV
Retrocopy SLGSAGHTTLGVTLMIGGLTCVLSLICALVLAYLDQRAERILHKEQGKTGEVIKLTNVKDFSLPLWLIFV

Parental  ICVCYYVVVFPFIGLGKVFFTEKFGFSSQAASAINSIVYVISAPMSPVFGLLVDKTGKNIIWVLCAVAAT
          ICVCYYVVVFPF.GLGKVFFTEKFGFSSQA..AINSIVYVISAPMSPVFGLLVDKTGKNIIWVLCAVAA.
Retrocopy ICVCYYVVVFPFTGLGKVFFTEKFGFSSQAGRAINSIVYVISAPMSPVFGLLVDKTGKNIIWVLCAVAAA

Parental  L-VSHMMLAFTMWNPWIAMCLLGLSYSLLACALWPMVAFVVPEHQLGTAYGFMQSIQNLGLAVISIIAGM
          L.VSHM.LAFTMWNPWIAMCLLGLSYSLLACALWPMVAFVVPEHQLGTAYGFMQSIQNLGLAVISIIAGM
Retrocopy L<VSHMKLAFTMWNPWIAMCLLGLSYSLLACALWPMVAFVVPEHQLGTAYGFMQSIQNLGLAVISIIAGM

Parental  ILDTRGYLFLEVFFIACVSLSLLSVVLLYLVDRARGGNLNYSARQREEMKMSHTE
          ILDT.GYLFL.V.FIACVSLSLLSVVLLY.VD.ARGGNLNYSARQREEMKMSHTE
Retrocopy ILDTQGYLFL-VYFIACVSLSLLSVVLLYFVDHARGGNLNYSARQREEMKMSHTE

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	0.77 RPM	22.02 RPM
SRP017611_kidney	1.62 RPM	40.75 RPM
SRP017611_liver	0.46 RPM	13.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1528 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1528 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528 ,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,