RetrogeneDB ID: retro_ocun_1394

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:172220167..172220533(-)
• Located in intron of: ENSOCUG00000016930

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS16
• Ensembl ID: ENSOCUG00000002150
• Aliases: None
• Description: ribosomal protein S16 [Source:HGNC Symbol;Acc:10396]

Sequence

>retro_ocun_1394
AGTACGGCCGCAGCCAGGCCGTCCAAGGGCCCACTACAGTCTGTTCAGGTCTTCGGACGGAAGGAGGCAGCTACCGCCGC
GGTGCACTGCAAACTGGGCAATGGGGGCTTATCAGGCTGAACGGAGGCCCCTGGAGATGATCAAGCCACACCCACCGCAG
TACAAGCTGTGCAGCAAGGAATGGTTTGCTGGCCTGGACATCCGTGTCCGAGTGAAGGGTGGTGGGCAGGACGCTCGGAT
GTATGCTATCTGCCAGTCCACTACATAGCCCTGGTGGCCTATCACCAGAAATATGCGGATGAGGCTTCCAGGAAGGAGAT
CAAAGACATCCTCAGCCAGTATGACCGCCCCCTGCTGGTAGCTAAC

Alignment

ORF - retro_ocun_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 74.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSAAAMPSKGPLQSVQVFGRKKTATAVAHCKRGN-GLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFA
          S.AAA.PSKGPLQSVQVFGRK..ATA..HCK.GN.G......RPLEMI.P...QYKL.......G.....
Retrocopy STAAARPSKGPLQSVQVFGRKEAATAAVHCKLGN>GAYQAERRPLEMIKPHPPQYKLCSKEWFAGLD---

Parental  GVDIRVRVKGGGHVAQIYAIRQSIS-KALVAYYQKYVDEASKKEIKDILIQYDRTLLVAD
          ....RV...GGG..A..YAI.QS....ALVAY.QKY.DEAS.KEIKDIL.QYDR.LLVA.
Retrocopy -IRVRVK--GGGQDARMYAICQSTT<IALVAYHQKYADEASRKEIKDILSQYDRPLLVAN

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	68.99 RPM
SRP017611_kidney	0.10 RPM	174.43 RPM
SRP017611_liver	0.08 RPM	44.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1394 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1394 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014176	1 retrocopy	retro_acar_194,
Bos taurus	ENSBTAG00000021093	3 retrocopies	retro_btau_1509, retro_btau_167, retro_btau_441,
Canis familiaris	ENSCAFG00000005501	6 retrocopies	retro_cfam_1349, retro_cfam_1754, retro_cfam_2142, retro_cfam_2147, retro_cfam_799, retro_cfam_908,
Callithrix jacchus	ENSCJAG00000014170	6 retrocopies	retro_cjac_2641, retro_cjac_2737, retro_cjac_3019, retro_cjac_885, retro_cjac_905, retro_cjac_949,
Cavia porcellus	ENSCPOG00000011359	3 retrocopies	retro_cpor_1266, retro_cpor_1408, retro_cpor_1515,
Equus caballus	ENSECAG00000004311	2 retrocopies	retro_ecab_186, retro_ecab_779,
Felis catus	ENSFCAG00000010743	4 retrocopies	retro_fcat_1258, retro_fcat_1709, retro_fcat_1806, retro_fcat_1976,
Gorilla gorilla	ENSGGOG00000014414	10 retrocopies	retro_ggor_110, retro_ggor_1250, retro_ggor_1344, retro_ggor_1664, retro_ggor_1766, retro_ggor_193, retro_ggor_2423, retro_ggor_2819, retro_ggor_652, retro_ggor_667,
Loxodonta africana	ENSLAFG00000001541	1 retrocopy	retro_lafr_1191,
Macaca mulatta	ENSMMUG00000019370	8 retrocopies	retro_mmul_1018, retro_mmul_1080, retro_mmul_1175, retro_mmul_1219, retro_mmul_1403, retro_mmul_20, retro_mmul_767, retro_mmul_862,
Monodelphis domestica	ENSMODG00000013545	4 retrocopies	retro_mdom_1668, retro_mdom_1823, retro_mdom_815, retro_mdom_856,
Nomascus leucogenys	ENSNLEG00000014388	3 retrocopies	retro_nleu_1266, retro_nleu_248, retro_nleu_46,
Oryctolagus cuniculus	ENSOCUG00000002150	14 retrocopies	retro_ocun_1028, retro_ocun_1073, retro_ocun_1394 , retro_ocun_1430, retro_ocun_1436, retro_ocun_1774, retro_ocun_371, retro_ocun_580, retro_ocun_632, retro_ocun_645, retro_ocun_670, retro_ocun_837, retro_ocun_906, retro_ocun_986,
Otolemur garnettii	ENSOGAG00000004497	4 retrocopies	retro_ogar_1229, retro_ogar_1309, retro_ogar_1313, retro_ogar_98,
Oreochromis niloticus	ENSONIG00000000006	1 retrocopy	retro_onil_52,
Pelodiscus sinensis	ENSPSIG00000016930	1 retrocopy	retro_psin_55,
Rattus norvegicus	ENSRNOG00000019578	3 retrocopies	retro_rnor_10, retro_rnor_1823, retro_rnor_302,
Sus scrofa	ENSSSCG00000010712	1 retrocopy	retro_sscr_731,
Sus scrofa	ENSSSCG00000020817	3 retrocopies	retro_sscr_478, retro_sscr_5, retro_sscr_723,