RetrogeneDB ID: retro_ocun_635

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:16769016..16769957(-)
• Located in intron of: ENSOCUG00000026059

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENDOG
• Ensembl ID: ENSOCUG00000021275
• Aliases: None
• Description: endonuclease G [Source:HGNC Symbol;Acc:3346]

Sequence

>retro_ocun_635
ATGCGGAAGCTGCGGGCCGCTCTCACCCTGACGCTGGGTGCGGGGCTGGGCGCCGCCGCCAAGAGCTGGCGGCGGCGGCG
GGCGGACGCGTGGCCGGCTCACGGACTGCCGGGCCGGCTGCCCGTGCTGCCCGTGGCCGCGGCGGCTGAGCTGCCCGCCC
TCCCTTGGGACGCGGGGGCCGTTCGGCGGGCGAGCTGGCCAAGTACGGGCTGCCTAGGGTGGCGCAGCTCCAGAGCCGCG
AGTCGTACCTGCTGTGCTAGGACGCGCACACCCGCGGCGCGCTCTGGGTGGTGGAGCAGCTGCGGCCCGAGCGGCTGCGG
GGCGCCGGCGACCGGCGCTCGTGCGACTTCCGCGAGGACAACTAGGTGCACGCGTACCACCGCGCCACCAGTGCCGACTA
CCGCGGCAGCGGCTTCGACCGCGGACACCTCGCCGCCGCCGCCAACCACCGCTGGAGCCAGAAGGCGTGGACGACACCTA
CTACCTGAGCAACATGGCGCCCCAGGTGCCCCCCACCCCCAACCAGAACGCCAGTAACAACCTGGGGAAGTACAGCCGCA
GCTTGACCCGCACCGACCAGACATCTACGTGTGCACTGGGCCGCTCTTCCTGCCCAGGATGGAGGCCGACGGGAAGGCCT
ATGTGAACTACCAGGTGATCGGCAAGAACCACGTGGTGGTGCCCACGCACTTCTTCAAGTGCCCACGTCATTCCTGGAGG
CGGCGGGTGGGCAGGTCGAGCTGCGTTCCCACGGGATGCCCAAGGCGCCCGTGGAGGAGGCCATCCCGCTGGAGCGCCTC
CTGGTGCCCATCAAGGAGCACTGAGCGGGTCTTGGGGCTGCTCTTCGTGCCCAACAGCCTGGCGCGGACCGGCTGCCTCA
AGGCCATCACTGCCGGCGGCAAGTGAGGGCGGCAGCCCAGAGGGACCGCGCTGGGGGCGGG

Alignment

ORF - retro_ocun_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.62 %
• Parental protein coverage: 97.8 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MRTLRAALTLTLGAGLGAVAESWRRQRADARPAPGLLGRLPVLPVAAAAELPALPGGAGA-RAAGELAKY
          MR.LRAALTLTLGAGLGA.A.SWRR.RADA.PA.GL.GRLPVLPVAAAAELPALP..AGA.R.AGELAKY
Retrocopy MRKLRAALTLTLGAGLGAAAKSWRRRRADAWPAHGLPGRLPVLPVAAAAELPALPWDAGA<RSAGELAKY

Parental  GLPGVAQLKSRESYVLCYDARTRGALWVVEQLRPERLRGAGDRRSCDFREDDSVHAYHRAC-QRRLPRQR
          GLP.VAQL.SRESY.LC.DA.TRGALWVVEQLRPERLRGAGDRRSCDFRED..VHAYHRA..Q.RLPRQR
Retrocopy GLPRVAQLQSRESYLLC*DAHTRGALWVVEQLRPERLRGAGDRRSCDFREDN*VHAYHRAT<QCRLPRQR

Parental  LRPRPPRRRRQPPLEPEG-HGRHLLPEQRGAPGAP-PQPERLEQPGEVHPQPDPHLPE-RLRVHRAALPA
          LRPR.PRRRRQPPLEPEG..GRHLLPEQ.GAPGAP.PQPER..QPGEV.PQ.DPH.P...LRVH.AALPA
Retrocopy LRPRTPRRRRQPPLEPEG<RGRHLLPEQHGAPGAPHPQPERQ*QPGEVQPQLDPHRPD<HLRVHWAALPA

Parental  QDGGRREGLCEVPGDRQEPRGGAHALLQ-GAH--PGGGGWADRAALLRDAQRARGRGPAAGALPGAH-RE
          QDGGRREGLCE.PGDRQEPRGGAHALLQ..AH..PGGGGWA.RAA..RDAQ.ARG.G..AGA.PGAH..E
Retrocopy QDGGRREGLCELPGDRQEPRGGAHALLQ<SAHVIPGGGGWAGRAAFPRDAQGARGGGHPAGAPPGAH>KE

Parental  HRAGLGAALRAQHPGADRQPQGHRCRRPVR-AGPRDRAGAG
          H.AGLGAALRAQ.PGADR.PQGH.CRR.VR.A..RDRAG.G
Retrocopy H*AGLGAALRAQQPGADRLPQGHHCRRQVRAAAQRDRAGGG

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	8.55 RPM
SRP017611_kidney	0.00 RPM	13.68 RPM
SRP017611_liver	0.08 RPM	7.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_635 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021275	1 retrocopy	retro_ocun_635 ,