RetrogeneDB ID: retro_ocun_1093

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:45928438..45929500(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED25
• Ensembl ID: ENSOCUG00000022380
• Aliases: None
• Description: mediator complex subunit 25 [Source:HGNC Symbol;Acc:28845]

Sequence

>retro_ocun_1093
GGTGGGCAGCAGTCAGTGTTAAACAAGCTGCTGGCCTGGAGCAGGGTCCTCGAATTGCAGAGAAACCTAAACCTGCTTTG
GTGGATGCCAACACCAAGTTGACGTAGTCCCTGCTATGCCAGGTCTACGTGTATCACAGGAAGAACCTGAAGATGAGCAG
TGGCCCAGAAGGGGATCATGTAGCTCACCACCTAGCAGGTGCTGACCACCCTGGGCCCATTGTTCCAGAACTCGAGGATG
GTGCATTTCCACTTCACCAAGAAGGACCTGGAGTCTCTGAAAGGCCTCTACCACATCATGGGCAATGGCTTCATGGGCTG
AGTGCACTTCCCTGATACGGTCCCATATGAGGTGTGCGTGCTCATGCTGCTGTACTTGTCGAAGAAGAAAATCTTCATGG
GCTTCATCTCCCATGACCAGAGTGGCTTTGTCAATGGCATCCAGAAGGTCCTCACCAACTACAATCAGGTGCAGCAGCAG
AAGCTGGAGTAGCAGTGGGGGATGAGAGGCAGCAGGTGTCCCCAGAGCTGGGCCCCATTCTGGAGAAATCTGGAGGTGAG
GCCCTCACAGAATCTGCTCCAGCTCTGCCCACCTCTGGGCACTGTGTGTGCCTCTGGGGCCATGAGGCAACCCCAGCCCC
AGGGCACTGCCCAGATCCCTCCAGGTGCCCCCTCCAGGGTCCTGCTGGCCCACTCCCTCCTGGACCTATCCTTTAGCTCC
AGAACCCTGGGTTCAACCCCCAGCTGTGAAGCCTCCTCCTCAACTCTCTGCTGCCCCAGACTGGGGTGCACCCCCAAGGC
CTCCCTCCAACACCTCCAGCCACCAGGGGCTCCCACACTGCTTCCCCCACCACACCAGGGCCCAGGTACCAGGGCCTGGG
GCAGCCCCAGCTGAGGCCCCCACTCCTGCACCCACCACCCACTCAGTCCTGGCCTGAGCAGCTGCCCCCGGAGGCTCCAT
TGCCAGGTCAGATGCTGCTGAGTGGGGGGTCCCTGGGGCCAGGTCCCCCAGCCGGGCCTGCAGCCCAGTGTCATGAACGA
TGACATCCTCATGGACCTCATC

Alignment

ORF - retro_ocun_1093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.22 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GGQQSVSNKLLAWSGVLEWQ-EKPKPASVDANTKLTRSLPCQVYVNHGENLKT-EQWP-QKLIMQLIPQQ
          GGQQSV.NKLLAWS.VLE.Q.EKPKPA.VDANTKLT.SL.CQVYV.H..NLK..EQWP.QK.IM.L...Q
Retrocopy GGQQSVLNKLLAWSRVLELQ<EKPKPALVDANTKLT*SLLCQVYVYHRKNLKM<EQWP<QKGIM*LTT*Q

Parental  LLTTLGPLFRNSRMVQFHFTNKDLESLKGLYRIMGNGFAGCVHFPHTAPCEVRVLMLLYSSKKKIFMGLI
          .LTTLGPLF.NSRMV.FHFT.KDLESLKGLY.IMGNGF.G.VHFP.T.P.EV.VLMLLY.SKKKIFMG.I
Retrocopy VLTTLGPLFQNSRMVHFHFTKKDLESLKGLYHIMGNGFMG*VHFPDTVPYEVCVLMLLYLSKKKIFMGFI

Parental  PYDQSGFVNGIRQVITNHKQVQQQKLEQQRGMGAQQAPPGLGPILED-QARPSQNLLQLRPPQPQPQGTV
          ..DQSGFVNGI..V.TN..QVQQQKLE.Q.GM.....P....P.......RPSQNLLQL.P....P.GTV
Retrocopy SHDQSGFVNGIQKVLTNYNQVQQQKLE*QWGMRGSRCPQSWAPFWRNLEVRPSQNLLQLCP----PLGTV

Parental  GASGTA-GQPQPQG---TSQTPPGAPQGPPGAAPGPAPPGPILRPQNPGANPQLRSLLLNPPPPQTGVPP
          .ASG...G.P.P.......Q.PP.....P......P..P.P...P......PQL........PP....PP
Retrocopy CASGAM>GNPSPRALPRSLQVPPPGSCWPTPSWTYPLAPEPWVQPPAVKPPPQLSAAPDWGAPPR---PP

Parental  PQASLHHLQP-PGAPTLLPPPHQGLGQPQLGPPLLHPPPTQSWPAQLPPRAPLPGQMLLSGGPRGPVPP-
          ...S.H...P....PT...P..QGLGQPQL.PPLLHPPPTQSWP.QLPP.APLPGQMLLSGG..GP.PP.
Retrocopy SNTSSHQGLP>TASPTTPGPRYQGLGQPQLRPPLLHPPPTQSWPEQLPPEAPLPGQMLLSGGSLGPGPP>

Parental  PGLQPSVMEDDILMDLI
          PGLQPSVM.DDILMDLI
Retrocopy PGLQPSVMNDDILMDLI

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	102.21 RPM
SRP017611_kidney	0.00 RPM	112.20 RPM
SRP017611_liver	0.00 RPM	38.61 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1093 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1093 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	ENSOCUG00000022380	1 retrocopy	retro_ocun_1093 ,