RetrogeneDB ID: retro_cfam_1011

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:20889340..20889921(+)
• Located in intron of: ENSCAFG00000004851

Retrocopy information

• Ensembl ID: ENSCAFG00000004857
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL19
• Ensembl ID: ENSCAFG00000016493
• Aliases: None
• Description: 60S ribosomal protein L19 [Source:UniProtKB/Swiss-Prot;Acc:D0VWQ5]

Sequence

>retro_cfam_1011
CTCAGGCTTCAGAAGAGGCTTGCCTCCAGTGTCCTCCGTTGTGGCAAAAAGAAGGTCTGGTTGGACCCCAATGAGACCAA
TGAAATCGCCAATGCAAACTCCCGTCAGCAGATACGAAAACTGATCAAAGATGGGCTGATAATCCGGAAGCCTGTGACTA
TCCATTCCCGAGCTCGGTGCCGGAAAAACGCTCTGGCCCGCCGGAAGGGCAGGCATATGGGCATTGGTAAGAGAAAAGGT
ACTGCCAATGCTCGAATGCCTGAGAAGGTAACGTGGATGAGGAGGATGAGAATTCTACGCAGGCTGCTCAGAAGATACCG
TGAATCTAAGAAGATTGACCGCCACATGTATCATAGCCTGTACCTGAAAGTGAAGGGTAACGTGTTCAAGAACAAGCGGA
TTCTCATGGAACACTTCCACAAGCTGAAGGCAGACAAGGCTCGCAAGAAGCTTCTGGCTGACCAGGCTGAGGCCTGCAGA
TCTAAGACCAAGGAGGCCCGCAAGCGCCGTGAAGAGCGCGGCTCCAGGCCAAGAAGGAGGAAATCATCAAGACTCTGTCC
AAGGAGGAAGAGACCAAGAAA

Alignment

ORF - retro_cfam_1011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKG
          LRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVT.HSRARCRKN.LARRKG
Retrocopy LRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTIHSRARCRKNALARRKG

Parental  RHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIH
          RHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEH.H
Retrocopy RHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHFH

Parental  KLKADKARKKLLADQAEARRSKTKEARK-RREE-RLQAKKEEIIKTLSKEEETKK
          KLKADKARKKLLADQAEA.RSKTKEARK.R.E..RLQAKKEEIIKTLSKEEETKK
Retrocopy KLKADKARKKLLADQAEACRSKTKEARKRREER<RLQAKKEEIIKTLSKEEETKK

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
SRP012049_cerebellum	2.23 RPM	477.69 RPM
SRP017611_brain	3.18 RPM	112.50 RPM
SRP017611_kidney	27.93 RPM	996.24 RPM
SRP017611_liver	0.44 RPM	226.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1011 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1011 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 135 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016493	14 retrocopies	retro_cfam_1011 , retro_cfam_1647, retro_cfam_1767, retro_cfam_1799, retro_cfam_1892, retro_cfam_2082, retro_cfam_2129, retro_cfam_328, retro_cfam_357, retro_cfam_486, retro_cfam_851, retro_cfam_909, retro_cfam_932, retro_cfam_940,
Choloepus hoffmanni	ENSCHOG00000006023	7 retrocopies	retro_chof_1041, retro_chof_1065, retro_chof_1135, retro_chof_1930, retro_chof_2567, retro_chof_338, retro_chof_993,
Callithrix jacchus	ENSCJAG00000008520	4 retrocopies	retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus	ENSDNOG00000019742	7 retrocopies	retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Equus caballus	ENSECAG00000025080	6 retrocopies	retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Macropus eugenii	ENSMEUG00000013900	10 retrocopies	retro_meug_1047, retro_meug_1201, retro_meug_1226, retro_meug_1256, retro_meug_1262, retro_meug_1486, retro_meug_1878, retro_meug_2108, retro_meug_2155, retro_meug_82,
Macaca mulatta	ENSMMUG00000004235	2 retrocopies	retro_mmul_283, retro_mmul_63,
Mustela putorius furo	ENSMPUG00000015041	5 retrocopies	retro_mputfur_1221, retro_mputfur_1248, retro_mputfur_1479, retro_mputfur_357, retro_mputfur_688,
Nomascus leucogenys	ENSNLEG00000000748	19 retrocopies	retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Pongo abelii	ENSPPYG00000008492	20 retrocopies	retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Tursiops truncatus	ENSTTRG00000006687	4 retrocopies	retro_ttru_1131, retro_ttru_1132, retro_ttru_1389, retro_ttru_1804,