RetrogeneDB ID: retro_ocun_511

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:73159897..73162458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZZZ3
• Ensembl ID: ENSOCUG00000002167
• Aliases: None
• Description: zinc finger, ZZ-type containing 3 [Source:HGNC Symbol;Acc:24523]

Sequence

>retro_ocun_511
TCACCAAAGAAGAGACCAGAGCCTGTGCAAATTCAGAAAGGAAACAACAATGGAAGAACCACTGATTTAAAACAGCAAAG
TGCTCGGGAGTCATGGGTAAGCCCTAGGAAAAGAGGACTGTCTTCTTCAGAAAAGGATAACTTAGAAAGGCAGGCTGTAG
AAAATTGTGAGAGAAAGCAAACAGAACCTGTTTCACCAGTTTTAAAAAGAATTAAGCATTGTCTTAGATCTGAAGCACCA
AACAGTTCAGAGGAAGATTCACCTATAAAATCAGACAAGGAGTCAGTAGAACAGAGGAGTACAGTAGTGGACAATGATGC
AGATTTTCAAGGGACGAAACGAGCTTCTCTATGTCTTATACTGGATGATTGTGAGAAAAGGGAAATTAAAAAGGTGAATC
TCAGTGAGCAAGGGCCGCTTAATTCTGCAATAGTTGAAGAAATCACAGGCTATTTGACTGTCAATGGTGTTGATGACAGT
GATTCAGCTGTTATAAACTGTGATGACTGTCAGCCTGATGGGAACACTAAGCAAAATAGCACTGGTTCCTATGTGTTGCA
GGAAAAATCAGTAACTGAAAATGGGGATTCCGAAACCCAAACTTCAATGTTCCTTGGTAGTAGGAAGGAGGACAGTTACG
TAGACCATAACGTGCCTTGCACAAATTCAGAAGTGCAGGTCAAGTTGGAGGACCACAAAATAGTAACTGCCTGCCTGCCT
GTGGAACATGTTAATCAGCTGACTACTGAGCCAGCTACAGGCCCTGTTTCTGAAATTCAGTCATCTTTAAGGGATTCTGA
GGAAGAAGTAGATGTGGTGGGAGATAGCAATGCCTCAAAAGAGCAGTGTAACGAAAACACCAATAACGTCTTGGACACAG
CTCTTGAAAGTACACCAGTCTCTGGAGAATCAGAACCATCTTCTGTTCTAGACTGTGTTTCAGCTCAAATGATGTCTTTA
TCAGAACCTCAAGAACATCGCTATACCTTGAGAACTTCACCACGAAGGGCGGTACCCAGAGGTAGTCCCACTAAAAACAG
TTCTCCTTGCAGAGAAAATGGACAATTTGAGGAGAATAATCTTAGTCCCACTGAAACAAATCCAACTGTTAGTGATAATG
AAGTGAGTCTCTCACAAATCCTGATGAAATTTCTGAAAATGAAAAAGATAAATGTTGTGACTCTCAAAATTACGGAAGTG
ATGGACTAAGTAAGCCATCCTCAGAAGCAAGACTCAATATTGGACATTTGCCATCTGCCAAAGAGAGTGCCAATCAGCAC
ATTACAGAAGAGGAAGATGATGATCCTGATGTTTATTACTTTGAATCAGATCATGTGGCTCTGAAACACAACAAAGATTA
TCAGAGACTGTTACAGACGATTGCTGTACTCGAGGCTCAGCGTTCTCAAGCAGTCCAAGACCTTGAAAGTTTAGGCAAAC
ACCAGAGAGAAGCTCTAAAAAATCCCATTGGATTTGTGGAAAAACTCCAGAAGAAGGCTGATATAGGGCTTCCATATCCA
CAGAGAGTTGTTCAGTTGCCTGAAATTGTATGGGATCAATATACCAATAGCCTTGGAAACTTTGAAAGGGAATTTAAAAA
TCGTAAAAGACATACTAGGAGAGTTAAACTAGTTTTTGATAAAGTAGGTTTACCCGCTAGACCAAAAAGTCCTTTAGATC
CTAAGAAGGATGGAGAGTCTCTTTCATACTCTGTGTTGCCTTTGAGTGATGGTCCGGAAGGCTCACACAGTCGTCCTCAG
ATGATAAGAGGCTGCCTTTGTGATGATACCAAACCAGAAACATTTAACCAACTGTGGACTGTTGAAGAACAGAAAAAACT
TGAACAGCTACTCCTGAAATACCCTCCTGAAGAAGTAGAATCTCGACGCTGGCAGAAGATAGCAGATGAACTGGGCAATA
GGACGGCAAAACAGGTTGCGAGCTGAGTACAGAAGTATTTCATAAAGTTAACTAAAGCTGGCATTCCAGTCCCAGGCAGA
ACACCTAACTTATATATATACTCCAAAAAGTCTTCGTCAAGCAGAAGGCAGCACCCCCTTAATAAGCATCTCTTCAAACC
TTCCATGTTCATGACTTCTCATGAACCACCAGTGTATATGGATGAAGATGATGACCGATCCTGTTTTCACAGCCATATGA
ACACTGCTATTGAAGAGGCATCCGATGAAGAAAGTATTCCTATTATGTATAGGAATTTACCTGAATATAAAGAACTACTA
CAGTTTAAAAAGTTAAAGAAGCAGAAACTTCAGCAAATGCAGGCTGAAAGTGGATTTGTGCAGCATGTTGGCTTCAAGTG
TGATAACTGTGGCATAGAACCTATCCAGGGTGTTCGGTGGCACTGCCAGGGTTGTCCTCCAGAAATGTCTTTGGATTTCT
GTGATTCTTGTTCTGACTGCCTACATGAAACAGAAATCCACAAGGAAGATCAGCAATTAGAACCTATTTATAGGTCAGAG
ACATTCTTAGACAGAGACTACTGTGTGTCCCAGGGCACCAGTTATAATTACCTGGACCCCAACTACTTTCCAGCAAACAG
A

Alignment

ORF - retro_ocun_511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.71 %
• Parental protein coverage: 93.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPKKRPEPVQIQKGNNNGRTTDLKQQSARESWVSPRKRGLSSSEKDNLERQAVENCERKQTEPVSPVLKR
          SPKKRPEPVQIQKGNNNGRTTDLKQQSARESWVSPRKRGLSSSEKDNLERQAVENCERKQTEPVSPVLKR
Retrocopy SPKKRPEPVQIQKGNNNGRTTDLKQQSARESWVSPRKRGLSSSEKDNLERQAVENCERKQTEPVSPVLKR

Parental  IKRCLRSEAPNSSEEDSPIKSDKESVEQRSTVVDNDADFQGTKRACRCLILDDCEKREIKKVNLSEQGPL
          IK.CLRSEAPNSSEEDSPIKSDKESVEQRSTVVDNDADFQGTKRA..CLILDDCEKREIKKVNLSEQGPL
Retrocopy IKHCLRSEAPNSSEEDSPIKSDKESVEQRSTVVDNDADFQGTKRASLCLILDDCEKREIKKVNLSEQGPL

Parental  NSAIVEEITGYLTVNGVDDSDSAVINCDDCQPDGNTKQNSTGSYVLQEKSVTENGDSETQTSMFLDSRKE
          NSAIVEEITGYLTVNGVDDSDSAVINCDDCQPDGNTKQNSTGSYVLQEKSVTENGDSETQTSMFL.SRKE
Retrocopy NSAIVEEITGYLTVNGVDDSDSAVINCDDCQPDGNTKQNSTGSYVLQEKSVTENGDSETQTSMFLGSRKE

Parental  DSYVDHNVPCTNSEVQVKLEDHKIVTACLPVEHVNQLTTEPATGPVSEIQSSLRDSEEEVDVVGDSNASK
          DSYVDHNVPCTNSEVQVKLEDHKIVTACLPVEHVNQLTTEPATGPVSEIQSSLRDSEEEVDVVGDSNASK
Retrocopy DSYVDHNVPCTNSEVQVKLEDHKIVTACLPVEHVNQLTTEPATGPVSEIQSSLRDSEEEVDVVGDSNASK

Parental  EQCNENTNNVLDTALESTPVSGESEPSSVLDCVSAQMMSLSEPQEHRYTLRTSPRRAVPRGSPTKNSSPC
          EQCNENTNNVLDTALESTPVSGESEPSSVLDCVSAQMMSLSEPQEHRYTLRTSPRRAVPRGSPTKNSSPC
Retrocopy EQCNENTNNVLDTALESTPVSGESEPSSVLDCVSAQMMSLSEPQEHRYTLRTSPRRAVPRGSPTKNSSPC

Parental  RENGQFEENNLSPTETNPTVSDNV-SESLTNPDEISENEKDKCCDSQNYGSDGLSKPSSEARLNIGHLPS
          RENGQFEENNLSPTETNPTVSDN..SESLTNPDEISENEKDKCCDSQNYGSDGLSKPSSEARLNIGHLPS
Retrocopy RENGQFEENNLSPTETNPTVSDNE<SESLTNPDEISENEKDKCCDSQNYGSDGLSKPSSEARLNIGHLPS

Parental  AKESANQHITEEEDDDPDVYYFESDHVALKHNKDYQRLLQTIAVLEAQRSQAVQDLESLGKHQREALKNP
          AKESANQHITEEEDDDPDVYYFESDHVALKHNKDYQRLLQTIAVLEAQRSQAVQDLESLGKHQREALKNP
Retrocopy AKESANQHITEEEDDDPDVYYFESDHVALKHNKDYQRLLQTIAVLEAQRSQAVQDLESLGKHQREALKNP

Parental  IGFVEKLQKKADIGLPYPQRVVQLPEIVWDQYTNSLGNFEREFKNRKRHTRRVKLVFDKVGLPARPKSPL
          IGFVEKLQKKADIGLPYPQRVVQLPEIVWDQYTNSLGNFEREFKNRKRHTRRVKLVFDKVGLPARPKSPL
Retrocopy IGFVEKLQKKADIGLPYPQRVVQLPEIVWDQYTNSLGNFEREFKNRKRHTRRVKLVFDKVGLPARPKSPL

Parental  DPKKDGESLSYSVLPLSDGPEGSHSRPQMIRGRLCDDTKPETFNQLWTVEEQKKLEQLLLKYPPEEVESR
          DPKKDGESLSYSVLPLSDGPEGSHSRPQMIRG.LCDDTKPETFNQLWTVEEQKKLEQLLLKYPPEEVESR
Retrocopy DPKKDGESLSYSVLPLSDGPEGSHSRPQMIRGCLCDDTKPETFNQLWTVEEQKKLEQLLLKYPPEEVESR

Parental  RWQKIADELGNRTAKQVASRVQKYFIKLTKAGIPVPGRTPNLYIYSKKSSSSRRQHPLNKHLFKPSTFMT
          RWQKIADELGNRTAKQVAS.VQKYFIKLTKAGIPVPGRTPNLYIYSKKSSSSRRQHPLNKHLFKPS.FMT
Retrocopy RWQKIADELGNRTAKQVAS*VQKYFIKLTKAGIPVPGRTPNLYIYSKKSSSSRRQHPLNKHLFKPSMFMT

Parental  SHEPPVYMDEDDDRSCFHSHMNTAIEEASDEESIPIMYRNLPEYKELLQFKKLKKQKLQQMQAESGFVQH
          SHEPPVYMDEDDDRSCFHSHMNTAIEEASDEESIPIMYRNLPEYKELLQFKKLKKQKLQQMQAESGFVQH
Retrocopy SHEPPVYMDEDDDRSCFHSHMNTAIEEASDEESIPIMYRNLPEYKELLQFKKLKKQKLQQMQAESGFVQH

Parental  VGFKCDNCGIEPIQGVRWHCQDCPPEMSLDFCDSCSDCLHETEIHKEDHQLEPIYRSETFLDRDYCVSQG
          VGFKCDNCGIEPIQGVRWHCQ.CPPEMSLDFCDSCSDCLHETEIHKED.QLEPIYRSETFLDRDYCVSQG
Retrocopy VGFKCDNCGIEPIQGVRWHCQGCPPEMSLDFCDSCSDCLHETEIHKEDQQLEPIYRSETFLDRDYCVSQG

Parental  TSYNYLDPNYFPANR
          TSYNYLDPNYFPANR
Retrocopy TSYNYLDPNYFPANR

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	0.66 RPM	12.64 RPM
SRP017611_kidney	0.41 RPM	18.35 RPM
SRP017611_liver	0.85 RPM	7.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_511 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_511 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000039068	1 retrocopy	retro_mmus_3708,
Oryctolagus cuniculus	ENSOCUG00000002167	1 retrocopy	retro_ocun_511 ,