RetrogeneDB ID: retro_ocun_136

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:143650315..143650603(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027134
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000028195
• Aliases: None
• Description: None

Sequence

>retro_ocun_136
ATGGCCGACGAAAAGCCCAAGGAAGGAGTCAAGACTGAGAACAACGATCATATTAATTTGAAGGTGGCGGGGCAGGATGG
TTCTGTGGTGCAGTTTAAGATTAAGAGGCATACACCACTTAGTAAACTAATGAAAGCCTATTGTGAACGACAGGGTTTGT
CAATGAGGCAGATCAGATTCCGATTTGACGGGCAGCCAATCAATGAATCAGACACACCTGCACAGTTGGAAATGGAGGAC
GAAGATACGATTGATGTGTTCCAGCAGCAGACGGGCGGTGTCTACTGA

Alignment

ORF - retro_ocun_136 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINES
          MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINES
Retrocopy MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINES

Parental  DTPAQLEMEDEDTIDVFQQQTGGVY
          DTPAQLEMEDEDTIDVFQQQTGGVY
Retrocopy DTPAQLEMEDEDTIDVFQQQTGGVY

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	0.17 RPM	7.40 RPM
SRP017611_kidney	0.10 RPM	6.79 RPM
SRP017611_liver	0.00 RPM	0.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_136 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009189	13 retrocopies	retro_amel_1097, retro_amel_1125, retro_amel_1199, retro_amel_1263, retro_amel_1434, retro_amel_152, retro_amel_1665, retro_amel_276, retro_amel_35, retro_amel_616, retro_amel_653, retro_amel_662, retro_amel_722,
Canis familiaris	ENSCAFG00000004724	1 retrocopy	retro_cfam_484,
Cavia porcellus	ENSCPOG00000004581	9 retrocopies	retro_cpor_1029, retro_cpor_1297, retro_cpor_1496, retro_cpor_202, retro_cpor_357, retro_cpor_823, retro_cpor_838, retro_cpor_869, retro_cpor_894,
Homo sapiens	ENSG00000188612	2 retrocopies	retro_hsap_4036, retro_hsap_4095,
Gorilla gorilla	ENSGGOG00000023769	3 retrocopies	retro_ggor_101, retro_ggor_184, retro_ggor_2576,
Loxodonta africana	ENSLAFG00000025811	10 retrocopies	retro_lafr_104, retro_lafr_1222, retro_lafr_1240, retro_lafr_200, retro_lafr_254, retro_lafr_324, retro_lafr_36, retro_lafr_488, retro_lafr_858, retro_lafr_888,
Monodelphis domestica	ENSMODG00000007222	11 retrocopies	retro_mdom_1263, retro_mdom_1472, retro_mdom_1474, retro_mdom_1560, retro_mdom_1598, retro_mdom_1755, retro_mdom_237, retro_mdom_378, retro_mdom_517, retro_mdom_788, retro_mdom_986,
Mus musculus	ENSMUSG00000020738	19 retrocopies	retro_mmus_1498, retro_mmus_1772, retro_mmus_1903, retro_mmus_2050, retro_mmus_2323, retro_mmus_2475, retro_mmus_2492, retro_mmus_2590, retro_mmus_2767, retro_mmus_2917, retro_mmus_2974, retro_mmus_3209, retro_mmus_3414, retro_mmus_3630, retro_mmus_415, retro_mmus_611, retro_mmus_689, retro_mmus_818, retro_mmus_827,
Oryctolagus cuniculus	ENSOCUG00000021739	4 retrocopies	retro_ocun_1024, retro_ocun_1631, retro_ocun_1690, retro_ocun_321,
Oryctolagus cuniculus	ENSOCUG00000028195	5 retrocopies	retro_ocun_110, retro_ocun_136 , retro_ocun_175, retro_ocun_22, retro_ocun_46,
Pongo abelii	ENSPPYG00000029777	2 retrocopies	retro_pabe_164, retro_pabe_84,
Pan troglodytes	ENSPTRG00000042199	19 retrocopies	retro_ptro_1004, retro_ptro_1183, retro_ptro_1263, retro_ptro_135, retro_ptro_143, retro_ptro_1775, retro_ptro_2051, retro_ptro_2147, retro_ptro_2212, retro_ptro_2247, retro_ptro_2252, retro_ptro_2400, retro_ptro_2463, retro_ptro_2528, retro_ptro_2605, retro_ptro_2666, retro_ptro_2759, retro_ptro_3260, retro_ptro_65,
Sorex araneus	ENSSARG00000005720	8 retrocopies	retro_sara_156, retro_sara_158, retro_sara_175, retro_sara_389, retro_sara_70, retro_sara_717, retro_sara_749, retro_sara_93,
Sus scrofa	ENSSSCG00000017212	15 retrocopies	retro_sscr_1112, retro_sscr_1132, retro_sscr_1147, retro_sscr_1148, retro_sscr_123, retro_sscr_249, retro_sscr_277, retro_sscr_409, retro_sscr_591, retro_sscr_684, retro_sscr_754, retro_sscr_765, retro_sscr_814, retro_sscr_847, retro_sscr_969,