RetrogeneDB ID: retro_ocun_458

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:74314203..74315278(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADSS
• Ensembl ID: ENSOCUG00000013982
• Aliases: None
• Description: adenylosuccinate synthase [Source:HGNC Symbol;Acc:292]

Sequence

>retro_ocun_458
CGGAGGCAAAGGGGAGGCGACGGATCTGCTGGCGCGGGGCGGTGGCATCGTCCTGCCGGCCGCACAGTTGTGGACGCTGT
GGAATACGCGGTTCATCTTTTACCCGGTGGCATAATTAACCCAGACGTTACTGCGTTCTTTGGGAAAGGTGTAGTACTTC
ATCGACCAGGATTGTTTGAAGGGGCAGAGAAAAATGTTCAAACAAGGAAAAGGTCTGAAAGGCTCTTGGAAGAGGGCTTA
GCATACCTGGCAGAGCTCCTATGGTATTTGATTTCCATCAAGCAGTCGCTTGGTGTCCAGGAACCTCAGAGACAAGAACA
AGCAGGAAAAAATCGGGGGAGCCGTGTAAAAGGGCGTTAGCCCAGCTTATTCTTCGAAAGCTGCTGAGAGCGGGTAGAGG
CTGTGCAATCTTGTTTCTGACTTTGCTGGCCTCTCTGAGAAGTTCAAAGTTCCAACTAACGGGAACAGGTCTAGACAGCC
CTCTTTGGAAATGGTCATTGAAGGTGAGCTACCAAAATTAAAGGGTTATATGGAAAGGATTAAACCAATGATGAGAGATG
GAATTTATTTCCTTTTATGAGACCCTACATAGACCACCAAAGAAAATCTTGGCTGGAGGTGCAAACGCCTCACTCTGAGA
TACTGATTTGGGGACTTGCCCTTTTGTAATCTCTTCAAACCATATGGTAGGAGGTGTTTGTACAGGTTTGGGTATGGCCT
CCCAGAATTTTGGGAAGGTGTGTAGAGTTGTGAAAGCTTACACAACTACATTTGGTATTGGTGTATTTCCTACAGAGCAA
GACAATGAAATTGGAGAATTATTGCAAACATGAGGAAGAGGGTTTGCCGTAACACCATAAGGAAAGCAAGATGTGGCTGG
TTGGCCCTTGTTTTATTCAAATATGCACATATGATTAATGGATTTACTGCACTGGCACTTACCAAACTGGATATTTTGGA
TGTGTTTACGGAAATCAAAGTTGGAGTTACTTACAAGTTAGATGGTGCAATCATACCTCACTTCCCAGCAAACCAAGAAG
TCGTAAATAAGGTTGAAGTTCAATACAAGTCTCTC

Alignment

ORF - retro_ocun_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.52 %
• Parental protein coverage: 75.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RLKKDGDFSCYLIGGNNAGHTVVVDSVEYDFHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQ-KG
          R....GD.S.............VVD.VEY..HLLP.GIINP.VTAF.G.GVV.H.PGLFE.AEKNVQ..G
Retrocopy RRQRGGDGSAGAGRWHRPAGRTVVDAVEYAVHLLPGGIINPDVTAFFGKGVVLHRPGLFEGAEKNVQ>QG

Parental  KGLEGWEKR-LIISDRAHIVFDFHQAAD-GIQEQQRQEQAGKNLGTTKKG-IGPVYSSKAARSGLRMCDL
          KGL.G..KR.L.I..RA..VFDFHQA...G.QE.QRQEQAGKN.G...KG...P.YSSKAA.SG.R.C.L
Retrocopy KGLKGSWKR>LSIPGRAPMVFDFHQAVA>GVQEPQRQEQAGKNRGSRVKG>VSPAYSSKAAESG*RLCNL

Parental  VSDFDGFSERFKVLANQYKSIYPTLEIDIEGELQKLKGYMERIKPMVRDGVYFL-YEALHGPPKKILVEG
          VSDF.G.SE.FKV..N...S..P.LE..IEGEL.KLKGYMERIKPM.RDG.YFL.YE.LH.PPKKIL..G
Retrocopy VSDFAGLSEKFKVPTNGNRSRQPSLEMVIEGELPKLKGYMERIKPMMRDGIYFL>YETLHRPPKKILAGG

Parental  ANAALLDIDFGTYPFVTSSNCTVGGVCTGLGMPPQNVGEVYGVVKAYTTRVGIGAFPTEQDNEIGELLQT
          ANA.L.D.D.GT.PFV.SSN..VGGVCTGLGM..QN.G.V..VVKAYTT..GIG.FPTEQDNEIGELLQT
Retrocopy ANASL*DTDLGTCPFVISSNHMVGGVCTGLGMASQNFGKVCRVVKAYTTTFGIGVFPTEQDNEIGELLQT

Parental  RGREFGVT-TGRKRRCGWLDLVLLKYAHMINGFTALALTKLDILDMFTEIKVGVAYKLDGEIIPHFPANQ
          .GR.F.VT.T.RK.RCGWL.LVL.KYAHMINGFTALALTKLDILD.FTEIKVGV.YKLDG.IIPHFPANQ
Retrocopy *GRGFAVT<TIRKARCGWLALVLFKYAHMINGFTALALTKLDILDVFTEIKVGVTYKLDGAIIPHFPANQ

Parental  EVLNKVEVQYKTL
          EV.NKVEVQYK.L
Retrocopy EVVNKVEVQYKSL

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	36.42 RPM
SRP017611_kidney	0.00 RPM	35.17 RPM
SRP017611_liver	0.00 RPM	7.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_458 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017069	2 retrocopies	retro_cjac_2721, retro_cjac_452,
Homo sapiens	ENSG00000035687	1 retrocopy	retro_hsap_1826,
Monodelphis domestica	ENSMODG00000006559	1 retrocopy	retro_mdom_1431,
Oryctolagus cuniculus	ENSOCUG00000013982	1 retrocopy	retro_ocun_458 ,
Pongo abelii	ENSPPYG00000000057	1 retrocopy	retro_pabe_1496,
Pan troglodytes	ENSPTRG00000002178	1 retrocopy	retro_ptro_1167,