RetrogeneDB ID: retro_ocun_1758

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018856:409365..410351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT11
• Ensembl ID: ENSOCUG00000001289
• Aliases: None
• Description: septin 11 [Source:HGNC Symbol;Acc:25589]

Sequence

>retro_ocun_1758
CACATCCTGTGCGTCGGGGAGACGGGCATTGGCAAATCCACGTTAATGGACACCTTGTTCAACACCAAATTTGAGTGTGA
CCCGCTACTCACAATGAACCGGTTTCCGGTTGAAAGCCAGAAGTTATGAGCTTCAGGAAAGCAATATTCGCTGAAGTTAA
CCATTGTGGACACCGTGGGATTTGGAGATCAAACAAATAAAGATGACAGCTATAAGCCGATCGTGGAGTATATCGATGCC
CAGTTCGAGGCCTACCTGCAGGAGGAGTTGAAGATTAAGCGTTCTCTCTTCAGCCACCACGACACCCGGATCCACGCCTG
CCTCTACTTCATCACCCCCACTGGACATTCGCTGAAGTCCCTGGACCTGGTGACCATGAAAAAGCTGGACAGTAAGGCTA
ACATCACTCCGATCATTGCAAAAGCTGACACCGTTGCCAAGAATGAACTGCACAAATTCAGGAGCAAAATCATGAGTGAA
CTAGTGAGCAACGGGGTCCAGATATGCCAATTCCCCACGGATGAAGAGACGGTGGTGGAGATCAACGTGACCATGAGCGT
CCATCTGCCGTTTGCTGTGGTCAGCAGCACCGAGGAGGTGAAGATCGGCAACAAGATGGCCAAGGCCCGGCAGTACCCCT
GGGGCATGGTGCAGGTGGAAAACCATTGCGACTTTGTGAACCTGCGGGAGATGCTGATCCGCGTGGACATGGGGGACCTG
CACTAGCAGACCCACACCCGCCACTACGAGCTGTACCGGCGCTGTGAGCTCGAGGAGATGGGGTTCAAGGACACGGACCC
CGACAGCAAGCCCTTCAGTCTCCAGGAGATGTACGAAGCAAAGAGGAATGAATCCCCGGGAGAACTGCAGAAGAAGGAAG
AAGAAATGAGACAGATGTTCGTGATGAGAGTGAAGGAGAAAGAAGCGGAGCTTAAAGAGGCGGAGAAGGAGCTGACGAGA
AGTTCGACCTCCTAAAGCAGACCCAC

Alignment

ORF - retro_ocun_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.88 %
• Parental protein coverage: 70.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NILCVGETGIGKSTLMDTLFNTKFESDP-ATHNEP-GVRLKARSYELQESNVR-LKLTIVDTVGFGDQIN
          .ILCVGETGIGKSTLMDTLFNTKFE.DP.ATHNEP.G.RLKARSYELQESN.R.LKLTIVDTVGFGDQ.N
Retrocopy HILCVGETGIGKSTLMDTLFNTKFECDP<ATHNEP<GFRLKARSYELQESNIR<LKLTIVDTVGFGDQTN

Parental  KDDSYKPIVEYIDAQFEAYLQEELKIKRSLFNYHDTRIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNII
          KDDSYKPIVEYIDAQFEAYLQEELKIKRSLF..HDTRIHACLYFI.PTGHSLKSLDLVTMKKLDSK.NI.
Retrocopy KDDSYKPIVEYIDAQFEAYLQEELKIKRSLFSHHDTRIHACLYFITPTGHSLKSLDLVTMKKLDSKANIT

Parental  PIIAKADTIAKNELHKFKSKIMSELVSNGVQIYQFPTDEETVAEINATMSVHLPFAVVGSTEEVKIGNKM
          PIIAKADT.AKNELHKF.SKIMSELVSNGVQI.QFPTDEETV.EIN.TMSVHLPFAVV.STEEVKIGNKM
Retrocopy PIIAKADTVAKNELHKFRSKIMSELVSNGVQICQFPTDEETVVEINVTMSVHLPFAVVSSTEEVKIGNKM

Parental  AKARQYPWGVVQVENENHCDFVKLREMLIRVNMEDLREQTHTRHYELYRRCKLEEMGFKDTDPDSKPFSL
          AKARQYPWG.VQV..ENHCDFV.LREMLIRV.M.DL..QTHTRHYELYRRC.LEEMGFKDTDPDSKPFSL
Retrocopy AKARQYPWGMVQV--ENHCDFVNLREMLIRVDMGDLH*QTHTRHYELYRRCELEEMGFKDTDPDSKPFSL

Parental  QETYEAKRNEFLGELQKKEEEMRQMFVMRVKEKEAELKEAEKEL-HEKFDLLKRTH
          QE.YEAKRNE..GELQKKEEEMRQMFVMRVKEKEAELKEAEKEL..EKFDLLK.TH
Retrocopy QEMYEAKRNESPGELQKKEEEMRQMFVMRVKEKEAELKEAEKEL<DEKFDLLKQTH

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	0.88 RPM	38.58 RPM
SRP017611_kidney	0.51 RPM	19.66 RPM
SRP017611_liver	0.39 RPM	18.50 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1758 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543,
Callithrix jacchus	ENSCJAG00000014744	1 retrocopy	retro_cjac_2336,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224,
Oryctolagus cuniculus	ENSOCUG00000001289	1 retrocopy	retro_ocun_1758 ,
Otolemur garnettii	ENSOGAG00000005210	1 retrocopy	retro_ogar_2831,
Pan troglodytes	ENSPTRG00000016192	1 retrocopy	retro_ptro_2753,