RetrogeneDB ID: retro_ocun_1354

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:36887215..36889213(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF6
• Ensembl ID: ENSOCUG00000004470
• Aliases: None
• Description: DDB1 and CUL4 associated factor 6 [Source:HGNC Symbol;Acc:30002]

Sequence

>retro_ocun_1354
GCTGCCACCTCTGTAGCTCTTTGTCCACCAATACCATATTATCTTGCTGTAGGTTGTTCTGATAGCTCAGTACGAATATA
TGATCGTCGAATGCTGGGCACAAGAGCTACAGGGAATTATGCAGGGCGAGGAACTACTGGAATGGTTGCCCGTTTTATTC
CTTCCCATCTTAATAATAAATCCTGCAGAGTGACATCTCTATGTTACAGTGAAGATGGCCAAGAGATTCTCGTTAGTTAC
TCTTCAGATTACATATACCTTTTTGACCCAAAAGATGACACAACACGAGAACTTAAGACTCCTTCTGCAGAAGAGAGAAG
AGAAGAGTTACGACAACCGCCAGTTAAGCGTTTGAGACTTCGTGGTGATTGATCAGATACTGGACCCAGAGCAAGGCCTG
AGAGTGAACGAGAACGAGATGGAGAACAAAGTCCCAACGTGTCATTGATGCAGAGAATGTCTGACATGTTATCAAGATGG
TTTGAAGAAGCAAGTGAAGTTGCACAGAGTAATAGAGGACGAGGAAGATCTCAACCCAGAGGTGGAACAAGTCAGTCAGA
TGTTTTAGCTGTTCCTACTGTCCCATCAAGTCCTGATTTGGAAGTGGGTGAAACTGCAATGGATGTAGATGCTCCTTCTG
ATCAGTTGCTTCAGCCGTCTACATCTTCTACGGTATCAGCTCCAGCTCACTTAATCTCATCTTCCACAGAAAGCCCTCAT
TCTACTTCTTTGTTATCATCTCCAGACAGTGAACAGAGGCAGTCTGCTGAGGCTTCTGGGCACCATGCACATCATCAGTC
TGATAACAATAATGAAAAGCTGAGCCCCAAACCAGGGACAGGTGAACCAGTTTTAAGTTTGCACTACAGCACAGAAGGAA
CAACTACAAGCACAATAAAACTGAACTTTACAGATGAATGGAGCAGTACAGCCTCCAGTTCTAGAGGAAATGGGAGCCAT
TGCAAATCTGAGGGTCAGGAGGAATCCCTGGCCCCACAGAGCTCAGGGCCATCACCAGAAGGCGATAATGATACAACTTT
TGAAGAATCAACAGAACATGTGACAAAAAGTCAAGAAGGCACATCTGCAGAAAACCTAGATGAGAACAGTACAGATAAAG
CACAATCAGATACATTTACAGCTGAGCCATTGGGTTCCAACTCAGGAGAAAGGAATAACCTCAATCTTGATAGCCCCTGA
GAGGTTCCAGAAGAATCCTCTTTGTCTGCAAAAGGCAAGGAACCAGAAACTTCAGATCAGACTAGCACTGAGAGTACTTC
CAATCCAAATAACACCAATGCTGAGCCTCAGGCCCAAACAGAAGCCATCGAGCCTTCAGCTCATGAGGAAACATCAGCCA
GGGACGCTGCTCTTCAGGACACAGATGATAGTAATGATGACCCAGTCCTGATCCCAGGTGCAAGGTATCGAGCAGGACCT
GGTGATAGACGCTCTGCTGTTGCCCGCATTCAGGAGTTCTTCAGACGGAGAAAAGAAAGGAAAGAAATGGAAGAATTGGA
TACTTTGAACATTAGAAGGCCACTAGTAAAGATGGTTTATAAAGGCCATCGCAACTCCAGGACAATGATAAAAGAAGCCA
CTTTCTGGGGTGCTAACTTCGTCATGAGCGGCTCTGACTGTGGCCATATCTTCATCTGGGATCGGCACACTGCCGAGCAC
TTGATGCTTCTGGAAGCCGATAACCACGTGGTAAACTGCCTGCAGCCACATCCCTTCGACCCAATTCTAGCCTCGTCTGG
CATAGATTATGACATAAAGATCTGGTCACCACTAGAAGAGTCAAGGATTTTTAACCGAAAACTTGCTGATGAAGTTATAA
CTCGAAATGAACTCATGCTGGAAGAGACTAGAAATACCATTACAGTTCCAGCCTCTTTCATGTTAAGGATGTTGGCTTCA
CTGAATCATATCCGAGCAGACCGGTTGGAGGGTGACAGATCAGAAGGCTCTGGCCAGGAGAATGAAAATGAGGACGAG

Alignment

ORF - retro_ocun_1354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.31 %
• Parental protein coverage: 80.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AATSVAICPPIPYYLAVGCSDSSVRIYDRRMLGTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYS
          AATSVA.CPPIPYYLAVGCSDSSVRIYDRRMLGTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYS
Retrocopy AATSVALCPPIPYYLAVGCSDSSVRIYDRRMLGTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYS

Parental  EDGQEILVSYSSDYIYLFDPKDDTARELKTPSAEERREELRQPPVKRLRLRGDWSDTGPRARPESERERD
          EDGQEILVSYSSDYIYLFDPKDDT.RELKTPSAEERREELRQPPVKRLRLRGD.SDTGPRARPESERERD
Retrocopy EDGQEILVSYSSDYIYLFDPKDDTTRELKTPSAEERREELRQPPVKRLRLRGD*SDTGPRARPESERERD

Parental  GEQSPNVSLMQRMSDMLSRWFEEASEVAQSNRGRGRSRPREGGASQSDVSAVPTVPSSPDLEAGETAMDV
          GEQSPNVSLMQRMSDMLSRWFEEASEVAQSNRGRGRS.PR.GG.SQSDV.AVPTVPSSPDLE.GETAMDV
Retrocopy GEQSPNVSLMQRMSDMLSRWFEEASEVAQSNRGRGRSQPR-GGTSQSDVLAVPTVPSSPDLEVGETAMDV

Parental  DAPSDQLLQPSTSSTVSAPAHLTSSSTESPHSTSLLSSPDSEQRQSAEASGPHAHHQSDNNNEKLSPKPG
          DAPSDQLLQPSTSSTVSAPAHL.SSSTESPHSTSLLSSPDSEQRQSAEASG.HAHHQSDNNNEKLSPKPG
Retrocopy DAPSDQLLQPSTSSTVSAPAHLISSSTESPHSTSLLSSPDSEQRQSAEASGHHAHHQSDNNNEKLSPKPG

Parental  TGEPVLSLHYSTEGTTTSTIKLNFTDEWSSTASSSRGNGSHCKSEGQEESLAPQSSGPSPEGDNDTIAFE
          TGEPVLSLHYSTEGTTTSTIKLNFTDEWSSTASSSRGNGSHCKSEGQEESLAPQSSGPSPEGDNDT..FE
Retrocopy TGEPVLSLHYSTEGTTTSTIKLNFTDEWSSTASSSRGNGSHCKSEGQEESLAPQSSGPSPEGDNDT-TFE

Parental  ESTEHVTKSQEGTSAENLDENSTDKAQSDTFTAEPLESNSGERNNLNLDSPCEVPEESSLSAKGKEPETS
          ESTEHVTKSQEGTSAENLDENSTDKAQSDTFTAEPL.SNSGERNNLNLDSP.EVPEESSLSAKGKEPETS
Retrocopy ESTEHVTKSQEGTSAENLDENSTDKAQSDTFTAEPLGSNSGERNNLNLDSP*EVPEESSLSAKGKEPETS

Parental  DQTSTESTSNPNNTNAEPQAQTEAIEPSAHEETSARDAALQDTDDSDDDPVLIPGARYRAGPGDRHRRSA
          DQTSTESTSNPNNTNAEPQAQTEAIEPSAHEETSARDAALQDTDDS.DDPVLIPGARYRAGPGD..RRSA
Retrocopy DQTSTESTSNPNNTNAEPQAQTEAIEPSAHEETSARDAALQDTDDSNDDPVLIPGARYRAGPGD--RRSA

Parental  VARIQEFFRRRKERKEMEELDTLNIRRPLVKMVYKGHRNSRTMIKEANFWGANFVMSGSDCGHIFIWDRH
          VARIQEFFRRRKERKEMEELDTLNIRRPLVKMVYKGHRNSRTMIKEA.FWGANFVMSGSDCGHIFIWDRH
Retrocopy VARIQEFFRRRKERKEMEELDTLNIRRPLVKMVYKGHRNSRTMIKEATFWGANFVMSGSDCGHIFIWDRH

Parental  TAEHLMLLEADNHVVNCLQPHPFDPILASSGIDYDIKIWSPLEESRIFNRKLADEVITRNELMLEETRNT
          TAEHLMLLEADNHVVNCLQPHPFDPILASSGIDYDIKIWSPLEESRIFNRKLADEVITRNELMLEETRNT
Retrocopy TAEHLMLLEADNHVVNCLQPHPFDPILASSGIDYDIKIWSPLEESRIFNRKLADEVITRNELMLEETRNT

Parental  ITVPASFMLRMLASLNHIRADRLEGDRSEGSGQENENEDE
          ITVPASFMLRMLASLNHIRADRLEGDRSEGSGQENENEDE
Retrocopy ITVPASFMLRMLASLNHIRADRLEGDRSEGSGQENENEDE

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	2.98 RPM	23.79 RPM
SRP017611_kidney	2.13 RPM	20.07 RPM
SRP017611_liver	1.93 RPM	11.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1354 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1354 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143164	1 retrocopy	retro_hsap_1543,
Oryctolagus cuniculus	ENSOCUG00000004470	2 retrocopies	retro_ocun_1354 , retro_ocun_802,