RetrogeneDB ID: retro_ocun_600

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:17001308..17002796(+)
• 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_600
AGTTGTTTTAAGGGTCTGCAGGTGGAGGAAAATTTTGATATTGAAGTGTCAAAATCCTTAGACGGAAAAGATGCTATTCA
TAGTTTTAAGCTGAGTCGAAACCATGTGGACTGGCACAGTGTGGATGAAGTGTATCTTTACAGTGATGCAACAACATCTA
AAATCGCAAGAACAGTTACCCAAAAACTGGGATTTTCTAAAGCATCAAGTAGCGGGACCAGACTTCATAGAGGTTACCTA
GAAGAAGCCACGTTGGAAGATAAGCCATCGCAGACCACCCATATTGTGTTTGTTGTACATGCATTGGGCAGAAAATGGAC
CAAGGAAGAATCATCAAAAACACAGCCATGATGAGAGAGGCTGCAAGAAAAATAGAAGAAAGGCATTTTTCCAATCATGC
AACACATGTGGAATTTCTGCCTGTTGAGTGGTGGTCAAAACTTACTCTTGATGGAGACACTGTTGATTCCATTACCCCTG
ACAAAGTACGAGGGTTGGGGGACATGCTGAACAGCAGTGCCATGGACATAATGTATTACACCAGCCCTCTGTATAGAGAT
GAACTAGTTAAAGGCCTTCAGCAAGAGCTGAATCAATTATATTCCCTTTTCTGTTCTCAGAATCCCGACTTTGAAGAAAA
AGGGGGTAAAGTCTCCATCATGTCACGTTCCTTGGGCTGTGTAATCACTTACGATATAATGATGGCTGGAATCCAGTTCA
GCTTTATGAACAGTTGCTGCAGAAGGAAGAAGAGCTGCCTGATGAGTGATGGATGAGCTATGAAGAAAGAAATCTTCTTG
ATGACTGTATATAACAAAACGACAGCCGAGGGAAATAGAAGAACCGCTACATGGACTGAAGGCATCATCTGTATCACAAA
CGCCTGCCTTAAAATGTAAGATTGAGAACTTCTCCTGCATGGGATCCCCACTAGCAGTTTTTTTGGCATTGTGTGGCATC
TGCCCAGGAGACAATGGAAGTCAGGACCATATTCTGCCTAGAGAGATTTGTAACCGGTTACTAAATATCTTTCATCCTAC
AGATCCAGTGGCTTATCGATTAGAACCATTAATACTAAAACACTACAGCAGCATTTCACCTGTCCAGATCCACTGGTACA
ATACTTCAAACCCTCTACCTTATGAGCCCGTGAAGCCAAGCTTTCTCAACCCAGCCAAAGAATCTACCTCAGTTTCAGAG
GATGAAGGCGTTTCTGCCATCCCAAGCCCTGTGACCTCACCAGTCTTGTCCCGCAGACACTATGGAGAATCTATAACAAT
CATAGGCAAAGCAAGCATATCAGGGGCTGCTAGCATCGGAAAGGGACTTGGCGGAATGCTCTTCTCAAGATTTGGACATT
CATCTACATCGCAAGCATCCGAGACTTCAAAGGACTCCATAGAAGACGAGAAGAAGTCAGCTGCCTCACCGTCTACAACC
ACTGTGGCAACACAGACCCTACCACAGAGCAGCCCTGGCTTTCTGGAG

Alignment

ORF - retro_ocun_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.2 %
• Parental protein coverage: 53.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLFKWRGYKENTDAAGLKRKRSQ-AIHSFKLSRNHVDWHSVDEVYLYSDATTSKIARTVTQKLGFSKASS
          S.FK.....EN.D....K......AIHSFKLSRNHVDWHSVDEVYLYSDATTSKIARTVTQKLGFSKASS
Retrocopy SCFKGLQVEENFDIEVSKSLDGKDAIHSFKLSRNHVDWHSVDEVYLYSDATTSKIARTVTQKLGFSKASS

Parental  SGTRLHRGYVEEATLEDKPSQTTHIVFVVHG-IGQKMDQGRIIKNTAMMREAARKIEERHFSNHATHVEF
          SGTRLHRGY.EEATLEDKPSQTTHIVFVVH..IGQKMDQGRIIKNTAMMREAARKIEERHFSNHATHVEF
Retrocopy SGTRLHRGYLEEATLEDKPSQTTHIVFVVHA<IGQKMDQGRIIKNTAMMREAARKIEERHFSNHATHVEF

Parental  LPVEWRSKLTLDGDTVDSITPDKVRGLRDMLNSSAMDIMYYTSPLYRDELVKGLQQELNRLYSLFCSRNP
          LPVEW.SKLTLDGDTVDSITPDKVRGL.DMLNSSAMDIMYYTSPLYRDELVKGLQQELN.LYSLFCS.NP
Retrocopy LPVEWWSKLTLDGDTVDSITPDKVRGLGDMLNSSAMDIMYYTSPLYRDELVKGLQQELNQLYSLFCSQNP

Parental  DFEEKGGKVSIVSHSLGCVITYDIMT-GWNPVRLYEQLLQKEEELPDERWMSYEERNLLDE-LYITKRRL
          DFEEKGGKVSI.S.SLGCVITYDIM..GWNPV.LYEQLLQKEEELPDE.WMSYEERNLLD..LYITKR..
Retrocopy DFEEKGGKVSIMSRSLGCVITYDIMM<GWNPVQLYEQLLQKEEELPDE*WMSYEERNLLDD<LYITKRQP

Parental  REIEERLHGLKASSVSQTPALRFKVENFFCMGSPLAVFLALRGIRPGNTGSQDHILPREICNRLLNIFHP
          REIEE.LHGLKASSVSQTPAL..K.ENF.CMGSPLAVFLAL.GI.PG..GSQDHILPREICNRLLNIFHP
Retrocopy REIEEPLHGLKASSVSQTPALKCKIENFSCMGSPLAVFLALCGICPGDNGSQDHILPREICNRLLNIFHP

Parental  TDPVAYRLEPLILKHYSNISPVQIHWYNTSNPLPYEHMKPSFLNPAKESTSVSETEGISAIPSPVTSPVL
          TDPVAYRLEPLILKHYS.ISPVQIHWYNTSNPLPYE..KPSFLNPAKESTSVSE.EG.SAIPSPVTSPVL
Retrocopy TDPVAYRLEPLILKHYSSISPVQIHWYNTSNPLPYEPVKPSFLNPAKESTSVSEDEGVSAIPSPVTSPVL

Parental  SRRHYGESITNIGKASILGAASIGKGLGGMLFSRFGRSSTSQASETSKDSVEDEKKSAASPSTTTVATQT
          SRRHYGESIT.IGKASI.GAASIGKGLGGMLFSRFG.SSTSQASETSKDS.EDEKKSAASPSTTTVATQT
Retrocopy SRRHYGESITIIGKASISGAASIGKGLGGMLFSRFGHSSTSQASETSKDSIEDEKKSAASPSTTTVATQT

Parental  LPQSSSGFLD
          LPQSS.GFL.
Retrocopy LPQSSPGFLE

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	0.28 RPM	29.03 RPM
SRP017611_kidney	0.20 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_600 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_600 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,