RetrogeneDB ID: retro_ocun_1408

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:39124086..39125070(+)
• Located in intron of: ENSOCUG00000027232

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSOCUG00000015090
• Aliases: None
• Description: suppressor of variegation 3-9 homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17287]

Sequence

>retro_ocun_1408
CTGCAAAATCTCAAGTGCTTGTTACTGCTCCAGCAGTTCTCTAATGACAAGCATAATTATTCATCTCAGGTAAAAAATGC
AAAGCAATAATTCCAAAATATAATAAAGCTTTGAAACCTGCTGTTGCTGAGTACATTGTAAAGAAGACTAAACAGAGGAT
AGCTTTGCAGAGATGGTAAGATGAACTCAACAGAATAAAGATTCATAAAGGAATGATATTTGTTGAAAATACTATTGACT
TGGAGGGCCCACCTTCTGACTTCTATTACATCAATGAATACAAACCAGCTCCTGGAATCAGCTTAGTAAATGAAGCCACC
TTTGGTTGTTCACGCACAGATCGCTTCTTTGAGAAATAGTGTCCTGCTGAAGCTGGAGTTCTGTTGGCTTATAATAAAAA
CCAACAAATTAGAATCCCACGTGGCACCCCATTTATGAATGCAACTCGAGGTGCCGATGTGGACCTGATTGTCCCAAAAG
GATTGTACAAAAAGGTGCGCAATATTCACTTTGCATCTTTCAAACTAGCAATGACTGTGACTTGGGTGTAAAAACACTTA
TGAAGATTAAAAGAATGAGTTTTGTCATGAATATGTTGGAGAGGTAATCACAAGTGAAGAAGCTGAAAGACGTGGACAGT
TCTGTGACAACAAAGGAATAGCTTATCTCTTTGATCTGGATTATGAATCTGATGAATTCACAGTGGATGCAGCTCAATAT
GGAAATGTGTCTCATTTTGTAAATCACAGTTGTGACCCAAATCTTCAGGTGTTCAGTGTTTTCATTGATAACCTTGAAAT
TCATCTTCCACGAATAGCATTATTTTCTACAAGAACCATAAATGCTGGAGAAGAGCTCACTTTTGATTATCAAATGAAAG
GTCCTGGAGATGTATCTTCAGATTCTATTGACCACAGTCCAGCCAAAAAGAGGATCAGAACTGTATGAAAACGTGGAGCT
GTGACTTGCAGAGGTTACCTCAAC

Alignment

ORF - retro_ocun_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.49 %
• Parental protein coverage: 80.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQNLKCPLLLQQFSNDKHNYLSQVK-KCKAIIPKYNNKALKPAVAEYIVKKAKQRIALQRWQDELNRRKN
          LQNLKC.LLLQQFSNDKHNY.SQVK.KCKAIIPKYN.KALKPAVAEYIVKK.KQRIALQRW.DELNR.K.
Retrocopy LQNLKCLLLLQQFSNDKHNYSSQVK<KCKAIIPKYN-KALKPAVAEYIVKKTKQRIALQRW*DELNRIKI

Parental  HKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFEKCCPAEAGVLLAYNKNQQIR
          HKGMIFVENT.DLEGPPSDFYYINEYKPAPGISLVNEATFGCS.TD.FFEK.CPAEAGVLLAYNKNQQIR
Retrocopy HKGMIFVENTIDLEGPPSDFYYINEYKPAPGISLVNEATFGCSRTDRFFEK*CPAEAGVLLAYNKNQQIR

Parental  IPPGTP-IYECNSRCRCGPDCPNRIVQKGTQYSLCIFRTSNGCGWGVKTLVKIKRMSFVM-EYVGEVITS
          IP.GTP.IYECNSRCRCGPDCP.RIVQKG.QYSLCIF.TSN.C..GVKTL.KIKRMSFVM.EYVGEVITS
Retrocopy IPRGTP<IYECNSRCRCGPDCPKRIVQKGAQYSLCIFQTSNDCDLGVKTLMKIKRMSFVM<EYVGEVITS

Parental  EEAERRGQFYDNKGITYLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALF
          EEAERRGQF.DNKGI.YLFDLDYESDEFTVDAA.YGNVSHFVNHSCDPNLQVF.VFIDNL...LPRIALF
Retrocopy EEAERRGQFCDNKGIAYLFDLDYESDEFTVDAAQYGNVSHFVNHSCDPNLQVFSVFIDNLEIHLPRIALF

Parental  STRTINAGEELTFDYQMKGSGDISSDSIDHSPAKKRVRTVCKCGAATCRGYLN
          STRTINAGEELTFDYQMKG.GD.SSDSIDHSPAKKR.RTV.K.GA.TCRGYLN
Retrocopy STRTINAGEELTFDYQMKGPGDVSSDSIDHSPAKKRIRTV*KRGAVTCRGYLN

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	0.06 RPM	4.58 RPM
SRP017611_kidney	0.00 RPM	3.04 RPM
SRP017611_liver	0.00 RPM	1.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1408 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004696	1 retrocopy	retro_cfam_574,
Cavia porcellus	ENSCPOG00000008492	1 retrocopy	retro_cpor_1546,
Homo sapiens	ENSG00000152455	1 retrocopy	retro_hsap_3482,
Gorilla gorilla	ENSGGOG00000028243	1 retrocopy	retro_ggor_2348,
Microcebus murinus	ENSMICG00000002803	1 retrocopy	retro_mmur_340,
Nomascus leucogenys	ENSNLEG00000012108	1 retrocopy	retro_nleu_2202,
Oryctolagus cuniculus	ENSOCUG00000015090	1 retrocopy	retro_ocun_1408 ,
Ochotona princeps	ENSOPRG00000009465	1 retrocopy	retro_opri_1005,
Pongo abelii	ENSPPYG00000002106	1 retrocopy	retro_pabe_2877,
Tupaia belangeri	ENSTBEG00000006477	4 retrocopies	retro_tbel_2646, retro_tbel_3572, retro_tbel_852, retro_tbel_993,