RetrogeneDB ID: retro_ocun_260

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018720:350670..351708(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001672
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006093
• Aliases: None
• Description: None

Sequence

>retro_ocun_260
ATGCTGGCTGCAAGGCTTGTGTGTCTGCGGACACTGCCTTCCAGGGTTTTCCACCCAGCTTTCACCAAGGCTTCTCCCGT
TGTGAAGAATTCCATCACCAAGAAACAGTGGCTCATAACACCAAGCAGGGAATATGCCACCAAGACAAGAATTGGGGCTC
GACGTGGGAAAACTGGCCAAGACCTCAAAGAGGCAGCTTTGGAACCATCAGTGGAAAAAATATTTAAAATTGATCAGATG
GGAAGATGGTTTGTTGCTGGAGGGGCTGCTGTTGGTCTTGGAGCATTGTGCTACTATGGCTTGGGAATGTCTAATGAGAT
TGGAGCTATTGAAAAAGCTGTAATTTGGCCTCAGTATGTGAAAGATAGAATCCATTCTACCTACATGTACTTAGCAGGAA
GTATTGGTCTAACAGCTCTGTCTGCCATGGCAGTCACCAGGACTCCTGTCCTCATGAACTTCATGATGAAAGGCTCCTGG
GTGACCATTGGTGCAACCTTTGCAGCCATGATTGGAGCTGGAATGCTGGTACAGTCAATATCGTATGAGCAGAGCCCAGG
CCCAAAGCATCTTGCATGGCTGCTACATTCTGGTGTGATGGGTGCAGTAGTGGCTCCTCTGACAATTCTCGGGGGGCCTC
TTCTCATCAGAGCTGCATGGTACACAGCTGGCATTGTGGGAGGCCTCTCCACTGTGGCCATGTGTGCACCCAGTGAGAAG
TTTCTGAACATGGGAGCCCCGCTGGGAGTAGGCCTGGGTCTCGTCTTTGCGTCCTCTGTGGGATCTATGTTCCTGCCACC
AACCTCTGTGGCTGGTGCCACTTTGTACTCAGTGGCAGTGTACGGTGGATTAGTTCTCTTCAGTATGTTCCTTCTGTATG
ATACCCAGAAAGTAATCAAGCGTGCAGAAATAGCACCAATGTATGGAATTCAGAAATATGATCCCATCAATTCCATGCTG
GGAATCTACATGGATACGTTAAATATATTTATGCGAGTTGCAACTATGCTAGCAACTGGAAGCAACAGAAAGAAGTGA

Alignment

ORF - retro_ocun_260 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLAARLVCLRTLPSRVFHPAFTKASPVVKNSITKKQWLITPSREYATKTRIGARRGKTGQDLKEAALEPS
          MLAARLVCLRTLPSRVFHPAFTKASPVVKNSITKKQWLITPSREYATKTRIGARRGKTGQDLKEAALEPS
Retrocopy MLAARLVCLRTLPSRVFHPAFTKASPVVKNSITKKQWLITPSREYATKTRIGARRGKTGQDLKEAALEPS

Parental  VEKIFKIDQMGRWFVAGGAAVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAGSIGLTAL
          VEKIFKIDQMGRWFVAGGAAVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAGSIGLTAL
Retrocopy VEKIFKIDQMGRWFVAGGAAVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAGSIGLTAL

Parental  SAMAVTRTPVLMNFMMKGSWVTIGATFAAMIGAGMLVQSISYEQSPGPKHLAWLLHSGVMGAVVAPLTIL
          SAMAVTRTPVLMNFMMKGSWVTIGATFAAMIGAGMLVQSISYEQSPGPKHLAWLLHSGVMGAVVAPLTIL
Retrocopy SAMAVTRTPVLMNFMMKGSWVTIGATFAAMIGAGMLVQSISYEQSPGPKHLAWLLHSGVMGAVVAPLTIL

Parental  GGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGLVFASSVGSMFLPPTSVAGATLYSVAV
          GGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGLVFASSVGSMFLPPTSVAGATLYSVAV
Retrocopy GGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGLVFASSVGSMFLPPTSVAGATLYSVAV

Parental  YGGLVLFSMFLLYDTQKVIKRAEIAPMYGIQKYDPINSMLGIYMDTLNIFMRVATMLATGSNRKK
          YGGLVLFSMFLLYDTQKVIKRAEIAPMYGIQKYDPINSMLGIYMDTLNIFMRVATMLATGSNRKK
Retrocopy YGGLVLFSMFLLYDTQKVIKRAEIAPMYGIQKYDPINSMLGIYMDTLNIFMRVATMLATGSNRKK

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	8.94 RPM	42.00 RPM
SRP017611_kidney	9.53 RPM	46.02 RPM
SRP017611_liver	4.08 RPM	13.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_260 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_260 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260 ,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,