RetrogeneDB ID: retro_ocun_106

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:142702181..142702703(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000020937
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RBMX2
• Ensembl ID: ENSOCUG00000011809
• Aliases: None
• Description: RNA binding motif protein, X-linked 2 [Source:HGNC Symbol;Acc:24282]

Sequence

>retro_ocun_106
ATGAATCCGTTAACCAAGGTGAAGCTGGTGAGAGAGTTGAGTGAAAGGGAAGCTGGCATGGTGCCACCTAAGGTGTCCTG
GCACTCCATGTACCGGGACAGCGCTTGGGTCTTCGTGGGAGGGCTTCCGTATGAACTGACTGAAGGAGATATACTCTGTG
TGTTCTCGCAGTACGGGGAGATCGTTAACATTCATCTCGTGCGGGATAAGAAGACAGGGAAGTCTAGGGGGTTTGGTTTC
ATCTGCTATGAAGATCAGAGGAGTACGGTTTTGGCCGTTGACAATTTTAATGGAATCAAGATCAAGGGAAGAACTATCCG
GGTAGATCACGCGAGCAACTACCGCCCGCCTCGGGATTCAGAGGACATAGACGACGTCACCAGGGAGCTGCGGGAGAAGG
GCTGCGGGCCCCAGGTCCCCTCAGCGAGTTCATCTGGAGGCTCCAGGAACGAAGCGCTGCCACCGCAGCCCAAGCTAGAA
AAAGGGATGGGAGAAGACCAACGGGAGGACTGCTATAGGAGT

Alignment

ORF - retro_ocun_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.86 %
• Parental protein coverage: 51.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPLTKVKLINELNEREVQLGVAEKVSWHSEYKDSAWIFLGGLPYELTEGDVICVFSQNRYGEVVNINLVR
          .PLTKVKL..EL.ERE....V..KVSWHS.Y.DSAW.F.GGLPYELTEGD..CVFSQ..YGE.VNI.LVR
Retrocopy NPLTKVKLVRELSEREAGM-VPPKVSWHSMYRDSAWVFVGGLPYELTEGDILCVFSQ--YGEIVNIHLVR

Parental  DKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVANYRVPKVSEDMDDVTRELQAMGCGVN
          DKKTGKS.GF.F.CYEDQRST.LAVDNFNGIKIKGRTIRVDH..NYR.P..SED.DDVTREL...GCG..
Retrocopy DKKTGKSRGFGFICYEDQRSTVLAVDNFNGIKIKGRTIRVDHASNYRPPRDSEDIDDVTRELREKGCGPQ

Parental  TPSPSSSEDSEEEKPIKKHKKDKMEKKKRRKE
          .PS.SSS..S..E......K..K......R..
Retrocopy VPSASSSGGSRNEALPPQPKLEKGMGEDQRED

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	6.73 RPM
SRP017611_kidney	0.00 RPM	6.18 RPM
SRP017611_liver	0.00 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_106 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_106 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_664

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000017095	1 retrocopy	retro_mluc_310,
Oryctolagus cuniculus	ENSOCUG00000011809	1 retrocopy	retro_ocun_106 ,
Pteropus vampyrus	ENSPVAG00000004425	1 retrocopy	retro_pvam_1404,
Sarcophilus harrisii	ENSSHAG00000016412	1 retrocopy	retro_shar_2,
Tursiops truncatus	ENSTTRG00000016210	1 retrocopy	retro_ttru_1561,