RetrogeneDB ID: retro_ocun_1088

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:31381382..31381898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000027895
• Aliases: None
• Description: None

Sequence

>retro_ocun_1088
CTGAAGCAGACTGAACGATGAGCACCTGTTTTCAGCCCTGAGCGGCCGCTGACCATCTCAGAACCAAGCCTGGCTCTGAG
ACTGAAGAGCAAGAGAAGCACCTGGAGACAGATGCTGCCTGCATTGCCGTGACTCAGCTCAGAGGCAGATCCAGAGTCAG
GAGAAAATGCGCTCCACTCTCCTGGAGAAAATCAGCAGAGAGGACCAAGAATCAGAGAGTGGAGCTCTCCAGCCACACAA
GCAGACTTTTAACCCTGCAGACACCAAGACCCTGGGGGCTGCTGCTGCCTTCCAAAAGGGGACCACTGGACACCTTCAGG
GAGCAGTGGTCCTGGCCAGCCAGGAGCTGGAACAACCCTTGCAGGAGCCTGGGCACTATGGCAGGGACAGATGTCAGGAG
CTCCAGGCCAGCAGCATCAAATGCTCTGTGAGCTGCAAATGGCTCAAGGCAGGTGAATCAGGGAAAATGCCAAGTAGAAT
AAAAACCAGCATGAGTTGGCTTCAATGCACCCCTAC

Alignment

ORF - retro_ocun_1088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MRQTEGRVPVFSHE-VVPDHLRTKPDPEVEEQEKQLTTDAARIGA-DAAQKQIQSLNKMCSNLLEKISKE
          ..QTE...PVFS.E....DHLRTKP..E.EEQEK.L.TDAA.I...D.AQ.QIQS..KM.S.LLEKIS.E
Retrocopy LKQTER*APVFSPE<AAADHLRTKPGSETEEQEKHLETDAACIAV<DSAQRQIQSQEKMRSTLLEKISRE

Parental  ERESESGGLRPNKQTFNPADTNALVAAVAFG-KGLSNWRPSGSSGPGQPGQPGAGAILAGASGLQQVQMA
          ..ESESG.L.P.KQTFNPADT..L.AA.AF..KG...W.PSGSSG...PGQPGAG..LAGA..L.Q.QM.
Retrocopy DQESESGALQPHKQTFNPADTKTLGAAAAFQ<KG-DHWTPSGSSG---PGQPGAGTTLAGAWALWQGQMS

Parental  GAPGQQQPMLSGVQMAQ-AGQPGKMPSGIKTNI-KSASMHPY
          GAPGQQ..ML...QMAQ.AG..GKMPS.IKT.....ASMHPY
Retrocopy GAPGQQHQMLCELQMAQ>AGESGKMPSRIKTSM<ELASMHPY

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	13.96 RPM
SRP017611_kidney	0.00 RPM	10.74 RPM
SRP017611_liver	0.00 RPM	9.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1088 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1088 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1088 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458,
Erinaceus europaeus	ENSEEUG00000002286	1 retrocopy	retro_eeur_117,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088 , retro_ocun_67,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818,