RetrogeneDB ID: retro_ocun_802

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:55584686..55586789(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025753
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_802
TACTTTTCTATATCTTGTGGTGAAGATGGAACTGTTAGGTGGTTTGATACACGCATCAAAACTAGCTGCACAAAAGAAGA
TTGCAAAGATGACATTTTGATTAACTGTCACCGTGCTGCCACCTCTGTAGCTCTTTGTCCACCAATACCATATTATCTTG
ATGTAGGTTGTTCTGATAGCTCAGTACGAATATATGATCGTCGAATGCTGGGCACAAGAGCTACAGGGAATTATGCAGGG
CGAGGAACTACTGGAATGGTTGCCCGTTTTATTCCTTCCCATCTTAATAATAAATCCTGCAGAGTGACATCTCTATGTTA
CAGTGAAGATGGCCAAGAGATTCTCGTTAGTTACTCTTCAGATTACATATACCTTTTTGACCCAAAAGATGACACAGCGC
GAGAATTTAAGACTCCTTCTGCAGAAGAGAGAAGAGAAGAGTTACGACAACCGCCAGTTAAGTGTTTGAGACTTCGTGGT
GATTGGTCAGATACTGGACCCAGAGCAAGGCCTGAGAGTGAACGAGAACGAGATGGAGAACGAAGTCCCAACGTGTCATT
GATGCAGAGAATGTCTGACATGTTATCAAGATGGTTTGAAGAAGCAAGTGAAGTTGCACAGAGTAATAGAGGACGAGGAA
GATCTCGACCCAGAGGTGGAACAAGTCAGTCAGATGTTTCAGCTGTTCCTACTGTCCCATCAAGTCCTGATTTGGAAGTG
GGTGAAACTGCAATGGATGTAGATGCTCCTTCTGATCAGTTGCTTCAGCCATCTACATCTTCTACGGTATCAGCTCCAGC
TCACTTAACCTCATCTTCCACAAAAAGCCCTCATTCTACTTCTTTGTTATCATCTCCAGACAGTGAACAGAGGCAGTCTG
CTGAGGCTTCTGGGCACCATGCACATCATCAGTCTGATAACAATAATGAAAAGCTGAGCCCCAAACCAGGGACAGGTGAA
CCAGTTTTAAGTTTGCACTACAGCACAGAAGGAACAACTACAAGCACAATAAAACTGAACTTTACAGATGAGTGGAGCAG
TACAGCCTCCAGTTCTAGAGGAAATGGGAGCCATTGCAAATCTGAGGGTCAGGAGGAATCCCTGGCCCCACAGAGCTCAG
GGCCATCACCAGAAGGCGATAATGATACAACTTTTGAAGAATCAACAGAACATGTGACAAAAAGTCAAGAAGGCACATCT
GCAGAAAACCTAGATGAGAACAGGACAGATAAAGCACAATCAGATACATTTACAGCTGAGCCATTGGATTCCAACTCAGG
AGAAAGGAATAACCTCAATCTTGATAGCCCCTGTGAGGTTCCAGAAGAATCCTCTTTGTCTGCAAAAGGCAAGGAACCAG
AAACTTCAGATCAGACTAGCACTGAGAGTACTTCCAATCCAAATAACACCAATGCTGAGCCTCAGGCCCAAACAGAAGCC
ATCGAGCCTTCAGCTCATGAGGAAACAGCCAGGGACGCTGCTCTTCAGGACACAGATGATAGTGATGATGACCCAGTCCT
GATCCCAGGTGCAAGGTATCGAGCAGGACCTGGTGATAGACGCTCTGCTGTTGCCCGCATTCAGGAGTTCTTCAGACGGA
GAAAAGAAAGGAAAGAAATGGAAGAATTGGATACTTTGAACATTAGAAGGCCACTAGTAAAGATGGTTTATAAAGGCCAT
CGCAACTCCAGGACAATGATAAAAGAAGCCAATTTCTGGGGTGCTAACTTCGTCATGAGCGGCTCTGACTGTGGCCGTAT
CTTCATCTGGGATCGGCACACTGCCGAGCACTTGATGCTTCTGGAAGCCGATAACCACGTGGTAAACTGCCTGCAGCCAC
ATCCCTTCGACCCAATTCTAGCCTCGTCTGGCATAGATTATGACATAAAGATCTGGTCACCACTAGAAGAGATTTTTAAC
CGAAAACTTGCTGATGAAGTTATAACTCGAAATGAACTCATGCTGGAAGAGACTAGAAATACCATTACAGTTCCAGCCTC
TTTCATGTTAAGGATGTTGGCTTCACTGAATCATATCCGAGCAGACCGGTTGGAGGGTGACAGATCAGAAGGCTCTGGCC
AGGAGAATGAAAATGAGGACGAG

Alignment

ORF - retro_ocun_802 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.61 %
• Parental protein coverage: 85.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YTFLSCGEDGTVRWFDTRIKTSCTKEDCKDDILINCRRAATSVAICPPIPYYLAVGCSDSSVRIYDRRML
          Y...SCGEDGTVRWFDTRIKTSCTKEDCKDDILINC.RAATSVA.CPPIPYYL.VGCSDSSVRIYDRRML
Retrocopy YFSISCGEDGTVRWFDTRIKTSCTKEDCKDDILINCHRAATSVALCPPIPYYLDVGCSDSSVRIYDRRML

Parental  GTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYSEDGQEILVSYSSDYIYLFDPKDDTARELKTPS
          GTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYSEDGQEILVSYSSDYIYLFDPKDDTARE.KTPS
Retrocopy GTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYSEDGQEILVSYSSDYIYLFDPKDDTAREFKTPS

Parental  AEERREELRQPPVKRLRLRGDWSDTGPRARPESERERDGEQSPNVSLMQRMSDMLSRWFEEASEVAQSNR
          AEERREELRQPPVK.LRLRGDWSDTGPRARPESERERDGE.SPNVSLMQRMSDMLSRWFEEASEVAQSNR
Retrocopy AEERREELRQPPVKCLRLRGDWSDTGPRARPESERERDGERSPNVSLMQRMSDMLSRWFEEASEVAQSNR

Parental  GRGRSRPREGGASQSDVSAVPTVPSSPDLEAGETAMDVDAPSDQLLQPSTSSTVSAPAHLTSSSTESPHS
          GRGRSRPR.GG.SQSDVSAVPTVPSSPDLE.GETAMDVDAPSDQLLQPSTSSTVSAPAHLTSSST.SPHS
Retrocopy GRGRSRPR-GGTSQSDVSAVPTVPSSPDLEVGETAMDVDAPSDQLLQPSTSSTVSAPAHLTSSSTKSPHS

Parental  TSLLSSPDSEQRQSAEASGPHAHHQSDNNNEKLSPKPGTGEPVLSLHYSTEGTTTSTIKLNFTDEWSSTA
          TSLLSSPDSEQRQSAEASG.HAHHQSDNNNEKLSPKPGTGEPVLSLHYSTEGTTTSTIKLNFTDEWSSTA
Retrocopy TSLLSSPDSEQRQSAEASGHHAHHQSDNNNEKLSPKPGTGEPVLSLHYSTEGTTTSTIKLNFTDEWSSTA

Parental  SSSRGNGSHCKSEGQEESLAPQSSGPSPEGDNDTIAFEESTEHVTKSQEGTSAENLDENSTDKAQSDTFT
          SSSRGNGSHCKSEGQEESLAPQSSGPSPEGDNDT..FEESTEHVTKSQEGTSAENLDEN.TDKAQSDTFT
Retrocopy SSSRGNGSHCKSEGQEESLAPQSSGPSPEGDNDT-TFEESTEHVTKSQEGTSAENLDENRTDKAQSDTFT

Parental  AEPLESNSGERNNLNLDSPCEVPEESSLSAKGKEPETSDQTSTESTSNPNNTNAEPQAQTEAIEPSAHEE
          AEPL.SNSGERNNLNLDSPCEVPEESSLSAKGKEPETSDQTSTESTSNPNNTNAEPQAQTEAIEPSAHEE
Retrocopy AEPLDSNSGERNNLNLDSPCEVPEESSLSAKGKEPETSDQTSTESTSNPNNTNAEPQAQTEAIEPSAHEE

Parental  TSARDAALQDTDDSDDDPVLIPGARYRAGPGDRHRRSAVARIQEFFRRRKERKEMEELDTLNIRRPLVKM
          T.ARDAALQDTDDSDDDPVLIPGARYRAGPGD..RRSAVARIQEFFRRRKERKEMEELDTLNIRRPLVKM
Retrocopy T-ARDAALQDTDDSDDDPVLIPGARYRAGPGD--RRSAVARIQEFFRRRKERKEMEELDTLNIRRPLVKM

Parental  VYKGHRNSRTMIKEANFWGANFVMSGSDCGHIFIWDRHTAEHLMLLEADNHVVNCLQPHPFDPILASSGI
          VYKGHRNSRTMIKEANFWGANFVMSGSDCG.IFIWDRHTAEHLMLLEADNHVVNCLQPHPFDPILASSGI
Retrocopy VYKGHRNSRTMIKEANFWGANFVMSGSDCGRIFIWDRHTAEHLMLLEADNHVVNCLQPHPFDPILASSGI

Parental  DYDIKIWSPLEESRIFNRKLADEVITRNELMLEETRNTITVPASFMLRMLASLNHIRADRLEGDRSEGSG
          DYDIKIWSPLEE..IFNRKLADEVITRNELMLEETRNTITVPASFMLRMLASLNHIRADRLEGDRSEGSG
Retrocopy DYDIKIWSPLEE--IFNRKLADEVITRNELMLEETRNTITVPASFMLRMLASLNHIRADRLEGDRSEGSG

Parental  QENENEDE
          QENENEDE
Retrocopy QENENEDE

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	3.37 RPM	23.79 RPM
SRP017611_kidney	2.23 RPM	20.07 RPM
SRP017611_liver	2.62 RPM	11.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_802 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_802 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
Homo sapiens	ENSG00000143164	1 retrocopy	retro_hsap_1543,
Oryctolagus cuniculus	ENSOCUG00000004470	2 retrocopies	retro_ocun_1354, retro_ocun_802 ,