RetrogeneDB ID: retro_ocun_124

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:32511185..32511794(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000009136
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021860
• Aliases: None
• Description: None

Sequence

>retro_ocun_124
ATGGGGACCGTGACCGACGACGAAATCATACGGAAGCGTCTCCTGATTGACGGGGATGGCGCAGGGGATGATCGGAGAAT
TAATCTGCTGGTGAAGAGTTTCCTTAAGTGGTGCGGCTCTGGCTCGCAGGAGGAGGGACACAGCCAGTACCAGCGTATGC
TGAGCACGCTGTGGCAATGTGAATTTTCCATGGGCAAAACGTTGCTGGTATACAACATGAATCTCAAAGAAATGGAGAAT
TATGAAAAAATTTACAAAGAAATCGAATGTAACATTGCTGGAGCGCATGAAAAAATTGCTGAGTGCAAAAAGCAAATTCT
TCAAGCAAAACAAATACGGAAAAATCGCCAAGAATACGATGCGTTAGCAAAGGTCATTGAGCAGCATCCAGACAGGCATG
AGACTTTAAAGAAACTAGAGTCTCTGGGGAAGGAGTTGGAGCGTCTTTCACACATTAAAGAGAGTGTTGAAGATAAGCTG
GAATTGAGACGTAAACAGTTTCATGCTCTTCTCAGTAACATCCAGGAACTGCAACAAACTTTGGAAAATGATGAGAAGCT
TCCAGAGACAGAAGCTCACAGAACAAGCGTGGAAGCAGATCCCAAGCCA

Alignment

ORF - retro_ocun_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.38 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEVIRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLR
          DE.IRKRLLIDGDGAGDDRRINLLVKSF.KWC.SGSQEEG.SQYQRMLSTL.QCEFSMGKTLLVY.MNL.
Retrocopy DEIIRKRLLIDGDGAGDDRRINLLVKSFLKWCGSGSQEEGHSQYQRMLSTLWQCEFSMGKTLLVYNMNLK

Parental  EMENYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLKELESLGKEL
          EMENYEKIYKEIEC.IAGAHEKIAECKKQILQAK.IRKNRQEYDALAKVI..HPDRHETLK.LESLGKEL
Retrocopy EMENYEKIYKEIECNIAGAHEKIAECKKQILQAKQIRKNRQEYDALAKVIEQHPDRHETLKKLESLGKEL

Parental  EHLSHIKESVEDKLELRRKQFHVLLSTIHELQQTLENDEKLSEVEEAQETSMEANPKP
          E.LSHIKESVEDKLELRRKQFH.LLS.I.ELQQTLENDEKL.E..EA..TS.EA.PKP
Retrocopy ERLSHIKESVEDKLELRRKQFHALLSNIQELQQTLENDEKLPET-EAHRTSVEADPKP

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	0.06 RPM	40.78 RPM
SRP017611_kidney	0.10 RPM	36.29 RPM
SRP017611_liver	0.08 RPM	15.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_124 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Equus caballus	ENSECAG00000000497	1 retrocopy	retro_ecab_1097,
Echinops telfairi	ENSETEG00000015076	3 retrocopies	retro_etel_1093, retro_etel_1858, retro_etel_85,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774,
Macropus eugenii	ENSMEUG00000006342	4 retrocopies	retro_meug_1481, retro_meug_1524, retro_meug_1599, retro_meug_1861,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Monodelphis domestica	ENSMODG00000003009	1 retrocopy	retro_mdom_315,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124 ,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Ochotona princeps	ENSOPRG00000016403	2 retrocopies	retro_opri_1031, retro_opri_345,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sarcophilus harrisii	ENSSHAG00000011615	1 retrocopy	retro_shar_240,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Ictidomys tridecemlineatus	ENSSTOG00000012552	1 retrocopy	retro_itri_1425,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,