RetrogeneDB ID: retro_ocun_1757

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018856:319402..320887(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDHD1
• Ensembl ID: ENSOCUG00000000326
• Aliases: None
• Description: DDHD domain containing 1 [Source:HGNC Symbol;Acc:19714]

Sequence

>retro_ocun_1757
AGTTGTTTTAAGGGTCGGCAGATGGAGGAAAATTCTGATATTGAAGTGTCAAAATCCTTAGAAAAGATGCTATTCATAGT
TTTAGGTTGAGTTGAAACCATGTGGACTGGCACAGTGTGGATGAAGTGTATCTTTACAGTAATGCAACAACATCTAAAAT
CGCAAGAACAGTTACCCAAAAACTGGGATTTTCTAAAGCATCAAGTAGCGGGACCAGACTTCATAGAGGTTACATAGAAG
AAGCCATGTTGGAAGATAAGCCATCGCAGACCACCCATATCATGTGTGTTGTACATGGCATTGGGCAGAAAATGGACCAA
GGAAGAATCATCAAAAACACAGCCATGATGAGAGAGGCTGCAAGAAAAATAGAAGAAAGGCGTTTTACCAATCATGCAAC
ACATGTGGAATTTCTGCCTGTTGAGTGGTGGTCAGAACTTACTCTTGACGGAGACACTGTTGATTCCATTACCCCTGACA
AAGTACGAGGGTTGGGGGACATGCTGAACAGCAGCGCCATGGACATAATGTATTACGCCAGCCCTCTTTATAGAGATGAA
CTAGTTAAAGGCCTTCAGCAAGAGCTGAATCAATTATATTCCCTTTTCTGTTCTCAGAATCCAGACTTTGAAGAAAAAGG
GGGTAAAGTCTCCATCATGTCACGTTCCTTGGGCTGTGTAATCACTTACGATATAATGATGGCTGGAATCCAGTTCAGCT
TTATGAACAGTTGCTGCAGAAGGAAGAAGAGCTGCCTGATGAGTGATGGATGAGCTATGAAGAAAGAAATCTTCTTGATG
ACTGTATATAACAAAACGACGGCTGAGGGAAATAGAAGAACGGCTACATGGACTGAAGGCATCATCTGTATCACAAACGC
CTGTCTTAAAATGTAAGATTGAGAATTTCTCCTGCATGGGATCCCCACTAGCAGTTTTTTTGGCATTGTGTGGCATCTGC
CCAGGAGACACTGGAAGTCAGGACCATATTCTGCCTAGAGAGATTTGTAACCGGTTACTAAATATCTTTCATCCTACAGA
TCCAGTGGCTTGTCGATTAGAACCATTAATACTAAAACACTACAGCAGCATTTCACCTGTCCAGATCCACTGGTACAATA
CTCCAAACCCTCTACCTCACGAGCCCGTGAAGCCAAGCTTTCTCAACCCAGCCAAAGAATCTACCTCAGTTTCAGAGAAT
GAAGGCGTTTCTGCCATCCCAAGCCCTGTGACCTCACCAGTCTTGTCCTGCTGACACTATGGAGAGTCTATAACAAACAT
AGGCAAAGCAAGCATATCAGGGGCTGCTGGCATTGGAAAGGGACTTGGCGGAATGCTCTTCTCAAGATTTGGACGTTCAT
CTGCATCGCAAGCATCTGAGACTTCAAAAGACTCCATAGAAGACGAGAAGAAGTCAGCTGCCTCACCGTCTACAACCACT
GTGGCAACACAGACCCTGCCACAGAGCAGCCCTGGCTTTCTGGAG

Alignment

ORF - retro_ocun_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.58 %
• Parental protein coverage: 53.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLFKWRGYKENTDAA-GLKRKRSQAIHSFKLSRNHVDWHSVDEVYLYSDATTSKIARTVTQKLGFSKASS
          S.FK.R...EN.D.....K..R..AIHSF.LS.NHVDWHSVDEVYLYS.ATTSKIARTVTQKLGFSKASS
Retrocopy SCFKGRQMEENSDIE<SVKILRKDAIHSFRLS*NHVDWHSVDEVYLYSNATTSKIARTVTQKLGFSKASS

Parental  SGTRLHRGYVEEATLEDKPSQTTHIVFVVHGIGQKMDQGRIIKNTAMMREAARKIEERHFSNHATHVEFL
          SGTRLHRGY.EEA.LEDKPSQTTHI..VVHGIGQKMDQGRIIKNTAMMREAARKIEER.F.NHATHVEFL
Retrocopy SGTRLHRGYIEEAMLEDKPSQTTHIMCVVHGIGQKMDQGRIIKNTAMMREAARKIEERRFTNHATHVEFL

Parental  PVEWRSKLTLDGDTVDSITPDKVRGLRDMLNSSAMDIMYYTSPLYRDELVKGLQQELNRLYSLFCSRNPD
          PVEW.S.LTLDGDTVDSITPDKVRGL.DMLNSSAMDIMYY.SPLYRDELVKGLQQELN.LYSLFCS.NPD
Retrocopy PVEWWSELTLDGDTVDSITPDKVRGLGDMLNSSAMDIMYYASPLYRDELVKGLQQELNQLYSLFCSQNPD

Parental  FEEKGGKVSIVSHSLGCVITYDIMT-GWNPVRLYEQLLQKEEELPDERWMSYEERNLLDE-LYITKRRLR
          FEEKGGKVSI.S.SLGCVITYDIM..GWNPV.LYEQLLQKEEELPDE.WMSYEERNLLD..LYITKRRLR
Retrocopy FEEKGGKVSIMSRSLGCVITYDIMM<GWNPVQLYEQLLQKEEELPDE*WMSYEERNLLDD<LYITKRRLR

Parental  EIEERLHGLKASSVSQTPALRFKVENFFCMGSPLAVFLALRGIRPGNTGSQDHILPREICNRLLNIFHPT
          EIEERLHGLKASSVSQTP.L..K.ENF.CMGSPLAVFLAL.GI.PG.TGSQDHILPREICNRLLNIFHPT
Retrocopy EIEERLHGLKASSVSQTPVLKCKIENFSCMGSPLAVFLALCGICPGDTGSQDHILPREICNRLLNIFHPT

Parental  DPVAYRLEPLILKHYSNISPVQIHWYNTSNPLPYEHMKPSFLNPAKESTSVSETEGISAIPSPVTSPVLS
          DPVA.RLEPLILKHYS.ISPVQIHWYNT.NPLP.E..KPSFLNPAKESTSVSE.EG.SAIPSPVTSPVLS
Retrocopy DPVACRLEPLILKHYSSISPVQIHWYNTPNPLPHEPVKPSFLNPAKESTSVSENEGVSAIPSPVTSPVLS

Parental  RRHYGESITNIGKASILGAASIGKGLGGMLFSRFGRSSTSQASETSKDSVEDEKKSAASPSTTTVATQTL
          ..HYGESITNIGKASI.GAA.IGKGLGGMLFSRFGRSS.SQASETSKDS.EDEKKSAASPSTTTVATQTL
Retrocopy C*HYGESITNIGKASISGAAGIGKGLGGMLFSRFGRSSASQASETSKDSIEDEKKSAASPSTTTVATQTL

Parental  PQSSSGFLD
          PQSS.GFL.
Retrocopy PQSSPGFLE

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	29.03 RPM
SRP017611_kidney	0.00 RPM	8.92 RPM
SRP017611_liver	0.00 RPM	4.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1757 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1757 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000326	2 retrocopies	retro_ocun_1757 , retro_ocun_600,
Otolemur garnettii	ENSOGAG00000017230	1 retrocopy	retro_ogar_281,