RetrogeneDB ID: retro_ocun_547

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:20213704..20214765(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSOCUG00000026953
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_ocun_547
CTCTTCAACGTCTATCCCTTTGTGCAAAGCTTCCTACAGCCCCACCAGAGAAGTAACGAAGATCCTTCTGTTTGCTGCAC
AAGCTTCTCATCACCTGGTGCCCCCAGAGATCATTCAGTCGTTGCTCATGACGGTGGCCAACAACTTTGTTACCGACAAG
AACTCTGGGGAAGTCCTGACCGTAGGCATCAATGCTATCAAAGAGGTAACAGCTCGGTGTCCTCTAGCCTCTAGCTGTTG
TTCACCTCCAAGACTTGGCTCAGTAGAAAACACACAAAGATAAGAATGTGATGATGGCTGCTAGAACTTTGATTCAGCTC
TTCCGCAACCTGAACCCACAGATGTTGCAGAAGAAATTCCGGGGTAAGCCTACGGAGGCCTCCACAGAGGCGCGAGCACA
GGAATATGGAGAATTAGATGCTAAAGATTATATTCCAGGAGCAGAAGTCTTGGAAGTTGAGAAAGAAGAGAATGCTGAAA
ATGATGAAGATGGGTGGGAAGGCACCAGTCTCAGTGAGGAGGACCAGGAGGATGCTGATGGGGAATGGTTGATGCGCACC
ACTCTTCCGACGAAGAACAGCAAGAAAGCGCCCGGGAGCTGAACAGCACGCCCATGGAGGAGCGCAAAGCCAAAGCTGCC
GCCTCAGCACCAGCTGGGTTTTGACTCAGGAAGACTTCCAGAAGATCTGCATTGCCCAGGGGAGGAAAGAACTGGACGCT
GCCCCTGGGAAAGCTGAGAAGAGGAAATATATTGAGAGAGAGAGTGACGAGGAACGCAGGGGCGAGTTACTGTCCCTTTG
GGATATTGAACGCATTCATAAAAAGCCAAAGTCTGACAAAGAGACAAGGCTGGCGACTGCAATGGCTGGGAAAACAGACT
GAAAGGAATTTGTGAGAAAGAAAACCAAAAGAACCCATTTGCTAGTTCCACAAATAAAGAGAAGAAAAAGCAGAAGAACT
TTCTGATGAGGCGGTATAGCCAGAATGTCCGGTCCAAAAACAAGTGTTCCTTCCGCGAAAAGCAACTGGCACTACGAGAT
GCACTTTTGAAAAAGAAAAAG

Alignment

ORF - retro_ocun_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.22 %
• Parental protein coverage: 51.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LFNFY-PFVQRFLQPHQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKE
          LFN.Y.P.......P..REVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEV.TVGINAIKE
Retrocopy LFNVY>PLCKASYSP-TREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVLTVGINAIKE

Parental  ITARCPLA-MTEELLQDLAQYKTHKDKNVMMAARTLIQLFRTLNPQMLQKKFRGKPTEASTEARVQEYGE
          .TARCPLA......LQDLAQ.KTHKDKNVMMAARTLIQLFR.LNPQMLQKKFRGKPTEASTEAR.QEYGE
Retrocopy VTARCPLA>LAVVHLQDLAQ*KTHKDKNVMMAARTLIQLFRNLNPQMLQKKFRGKPTEASTEARAQEYGE

Parental  LDAKDYIPGAEVLEVEKEENAENDEDGWESTSLSEEDEEDADGEW-VDVHHSSDEEQQEISRKLNSMPME
          LDAKDYIPGAEVLEVEKEENAENDEDGWE.TSLSEED.EDADGEW.VD.HHSSDEEQQE..R.LNS.PME
Retrocopy LDAKDYIPGAEVLEVEKEENAENDEDGWEGTSLSEEDQEDADGEW<VDAHHSSDEEQQESARELNSTPME

Parental  ERKAKAAA-VSTSRVLTQEDFQKIRIAQMRKELDAAPGKAEKRKYIEIDSDEERRGELLSLRDIERLHKK
          ERKAKAAA..STS.VLTQEDFQKI.IAQ.RKELDAAPGKAEKRKYIE..SDEERRGELLSL.DIER.HKK
Retrocopy ERKAKAAA<LSTSWVLTQEDFQKICIAQGRKELDAAPGKAEKRKYIERESDEERRGELLSLWDIERIHKK

Parental  PKSDKETRLATAMAGKTDRKEFVRKKTK-MNPFASSTNKEKKKQKNFMMMRYSQNVRSKNKRSFREKQLA
          PKSDKETRLATAMAGKTD.KEFVRKKTK..NPFASSTNKEKKKQKNF.M.RYSQNVRSKNK.SFREKQLA
Retrocopy PKSDKETRLATAMAGKTD*KEFVRKKTK<KNPFASSTNKEKKKQKNFLMRRYSQNVRSKNKCSFREKQLA

Parental  LRDALLKKRK
          LRDALLKK.K
Retrocopy LRDALLKKKK

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	12.75 RPM
SRP017611_kidney	0.30 RPM	12.26 RPM
SRP017611_liver	0.31 RPM	7.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_547 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547 ,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,