RetrogeneDB ID: retro_ocun_848

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:86561369..86562580(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSR1
• Ensembl ID: ENSOCUG00000014256
• Aliases: None
• Description: TSR1, 20S rRNA accumulation, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25542]

Sequence

>retro_ocun_848
ACCAGTTACCAAGCTGAATGGATTTCGGACGAAGATGGTGACATGGTGGGGAAGGAGATGAATGTGATGATACAGAACAT
GAGGAATTTTTGGATGGGGAATTTCAGAATAAGAGGGTGAAGTGGAAGAAGAGAAAGAATGTGTGAAACTATGACCAGAG
GGGACTCTGTAAGTGATGATGATCTGCATGATGAGAAAGTAGATGAAGAGGCTGAGGAAAAAATGGCAAAGTAGAAACTA
GAAAGACTCAAAGAGATGTTTCCAGGTACGTGGAAACCACCCCATGATGTGGCTGCCAGAATTTGATTTCAGAAATACAG
AGGTCTTAGGAGCTTCCAGACTTTTCGATGGGATCCTCAGAAAAACCTTCCTCAAGATTATACTCAGATCTTTCATTTTC
ACAACTTTACTAATCCTGGGAAAGGCATCTTGAGGGAGATTGATGAAGAGGTAGAAGGAGGTGAGGTTGGCTGGTGTGTC
ACACGTCACGTCTCTGATGTTCCTGTCTCAGTGGTGGAGCCCTTCAGGTGAGGAGCATTTGTAATCGCATTTTCTTTACT
CCCTCATCAACAGAAGATGTCAGTATTGAATACAGTGGTGAGGCAGGACCCTGGAGACACCGAACCTGTGAAAGCCAAAG
GGGAACTATCTTCCACTGTAGGTTCAGGTGCTTCTGAGCCTCTCTTTTATTCTCTCAGCACATTGCAGCAGGTAAACATA
AATTTCAGAGATTTCTAACTGCTGATGTGGACCTTGTGGTCATAGTATATATGCCAATCACTTTTCTTTCTGCATCTGTG
CTGCTTTTCAAACAGAAAAACAATGGGCACCTCATTGCTACAGGCCATCTGTCGTCGGTGGATCCAGACAGAATGGTCAT
CGAGAGAGTTGTTCTGAGTGGTTATCCTTTTAAAGGTTTTATGAAGATGGCAGTAGTGAGTCACATGTTCTTCAATAGAG
AGGATGTGCTGTGGTTTAAACCAGTGGAACTGAGAACAAAGTGGAGCTGAAGGAGACACATCAAAGAGCCTTTAGGTACC
TATGGCCACATGAAGTGCAGTTTTGATGGGAAGCTAAAATCTCAAGACATAGTAATGATGAACCTCTATCAATGAGTTCT
CTCCAAATGGACTTAGGATCTATATGTAGCAGAACCAGTACCTTGGGTAAAAAGTGAGATTTTTTTATCAGCGCTTGAAA
TGGACCCAGAA

Alignment

ORF - retro_ocun_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 50.43 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSYQAEWILDEDGDS-GGEGDEYDDTEHEDFMEEESQDESSEVEE-EEECETMTVGDSVRDD-LYDENVD
          .SYQAEWI.DEDGD..GGEGDE.DDTEHE.F...E.Q.........E..CETMT.GDSV.DD.L.DE.VD
Retrocopy TSYQAEWISDEDGDM<GGEGDECDDTEHEEFLDGEFQNKRVKWKK>ERMCETMTRGDSVSDDDLHDEKVD

Parental  EEAEEKMLEKYKQERLEEMFPDEVDTPRDVAARIRFQKYRGLKSFRTSPWDPKENLPRDYARIFQFQNFA
          EEAEEKM..K.K.ERL.EMFP.....P.DVAARI.FQKYRGL.SF.T..WDP..NLP.DY..IF.F.NF.
Retrocopy EEAEEKMA-K*KLERLKEMFPGTWKPPHDVAARI*FQKYRGLRSFQTFRWDPQKNLPQDYTQIFHFHNFT

Parental  NTRKSIFKEIDDKEVEGAEVGWYVTLHVSDVPVSVVESFRRGAPMIAFSLLPHEQKMSVLNMVVRRNPGD
          N..K.I..EID..EVEG.EVGW.VT.HVSDVPVSVVE.FR.GA..IAFSLLPH.QKMSVLN.VVR..PGD
Retrocopy NPGKGILREIDE-EVEGGEVGWCVTRHVSDVPVSVVEPFR*GAFVIAFSLLPHQQKMSVLNTVVRQDPGD

Parental  TEPVKAKEEL-IFHCGFRRFRASPLFSQHTAADKHKFQRFLTADVALVVTVYAPITFPPASVLLFKQKSN
          TEPVKAK.EL.IFHC.FR.F.AS.LFSQH.AA.KHKFQRFLTADV.LVV.VY.PITF..ASVLLFKQK.N
Retrocopy TEPVKAKGEL<IFHCRFRCF*ASLLFSQHIAAGKHKFQRFLTADVDLVVIVYMPITFLSASVLLFKQKNN

Parental  GMHNLIATGHLLSVDPDRMVIKRVVLSGHPFKIFTKTAVVRYMFFNREDVLWFKPVELRTKWGRRGHIKE
          G...LIATGHL.SVDPDRMVI.RVVLSG.PFK.F.K.AVV..MFFNREDVLWFKPVELRTKW..R.HIKE
Retrocopy G--HLIATGHLSSVDPDRMVIERVVLSGYPFKGFMKMAVVSHMFFNREDVLWFKPVELRTKWS*RRHIKE

Parental  PLGTHGHMKCSFDGKLKSQDTVLMNLYKRVFPKWTYDPYVPEPVPWIKSEIPSTVLEMDPE
          PLGT.GHMKCSFDGKLKSQD.V.MNLY..V..KWT.D.YV.EPVPW.KSEI....LEMDPE
Retrocopy PLGTYGHMKCSFDGKLKSQDIVMMNLYQ*VLSKWT*DLYVAEPVPWVKSEIFLSALEMDPE

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	0.00 RPM	39.74 RPM
SRP017611_kidney	0.00 RPM	47.03 RPM
SRP017611_liver	0.00 RPM	25.28 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_848 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_848 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019273	1 retrocopy	retro_cfam_104,
Cavia porcellus	ENSCPOG00000014833	2 retrocopies	retro_cpor_1258, retro_cpor_1307,
Oryctolagus cuniculus	ENSOCUG00000014256	1 retrocopy	retro_ocun_848 ,