RetrogeneDB ID: retro_cfam_1000

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:3443719..3444095(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000010615
• Aliases: None
• Description: Histone H2A [Source:UniProtKB/TrEMBL;Acc:F6X834]

Sequence

>retro_cfam_1000
GCTGGCGCTAAGGCGGGAAGGACTCCGGAGAGGCCAAGACCAGGGTGGTTTCTGGCTCACAGAGAGCCGGCTTGCGTTCC
CGGTGGCCCATATTCATCGACACCTGAAATCTAGGACGCCCAGCCACGGACCTGTGGGGCGCTGCCGCTGTGCACAGTGC
AGCCTTCCCGGGGTACCTCACCACAGAGGTGCTTGAATTGGCAGGAAATGCATCGAAAGACTTGAAGGTAAAGCGTATTA
CCCCTCGTCACTTGCAACTTGCTATTCGTGGAGAGGAAGAATTGGATTCATCATCAAGGCTACAAGTGCTGGTGGTGGTG
TTATTCCACACATCCACAAATCTCTGATTGGGAAGAAAGGACGACAGAAGACTGTT

Alignment

ORF - retro_cfam_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AGGKAG-KDSGKAKTKAVSRSQRAGLQ-FPVGRIHRHLKSRTTSHGRV-GATAAVYSAAILEYLTAEVLE
          AG.KAG.KDSG.AKT..VS.SQRAGL..FPV..IHRHLKSRT.SHG.V.GA.AAV.SAA...YLT.EVLE
Retrocopy AGAKAG<KDSGEAKTRVVSGSQRAGLR<FPVAHIHRHLKSRTPSHGPV>GA-AAVHSAAFPGYLTTEVLE

Parental  LAGNASKDLKVKRITPRHLQLAIRGDEELDS-LIKATIAGGGVIPHIHKSLIGKKGQQKTV
          LAGNASKDLKVKRITPRHLQLAIRG.EELDS..IKAT.AGGGVIPHIHKSLIGKKG.QKTV
Retrocopy LAGNASKDLKVKRITPRHLQLAIRGEEELDS<IIKATSAGGGVIPHIHKSLIGKKGRQKTV

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	0.00 RPM	64.89 RPM
SRP017611_brain	0.00 RPM	44.06 RPM
SRP017611_kidney	0.07 RPM	87.96 RPM
SRP017611_liver	0.00 RPM	8.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1000 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1000 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000959	1 retrocopy	retro_amel_1183,
Canis familiaris	ENSCAFG00000010615	2 retrocopies	retro_cfam_1000 , retro_cfam_101,
Callithrix jacchus	ENSCJAG00000015235	1 retrocopy	retro_cjac_91,
Echinops telfairi	ENSETEG00000006613	2 retrocopies	retro_etel_137, retro_etel_54,
Homo sapiens	ENSG00000164032	6 retrocopies	retro_hsap_1292, retro_hsap_2534, retro_hsap_2581, retro_hsap_4073, retro_hsap_4113, retro_hsap_598,
Gorilla gorilla	ENSGGOG00000027801	6 retrocopies	retro_ggor_1014, retro_ggor_137, retro_ggor_1616, retro_ggor_183, retro_ggor_2760, retro_ggor_720,
Loxodonta africana	ENSLAFG00000028460	2 retrocopies	retro_lafr_1255, retro_lafr_269,
Macropus eugenii	ENSMEUG00000013699	1 retrocopy	retro_meug_1457,
Microcebus murinus	ENSMICG00000002469	3 retrocopies	retro_mmur_1056, retro_mmur_1159, retro_mmur_634,
Macaca mulatta	ENSMMUG00000006834	7 retrocopies	retro_mmul_1049, retro_mmul_1320, retro_mmul_1593, retro_mmul_2368, retro_mmul_2448, retro_mmul_2465, retro_mmul_645,
Monodelphis domestica	ENSMODG00000020686	2 retrocopies	retro_mdom_1506, retro_mdom_977,
Mustela putorius furo	ENSMPUG00000009519	2 retrocopies	retro_mputfur_1343, retro_mputfur_1529,
Mus musculus	ENSMUSG00000037894	6 retrocopies	retro_mmus_2397, retro_mmus_2780, retro_mmus_2976, retro_mmus_3039, retro_mmus_3585, retro_mmus_953,
Nomascus leucogenys	ENSNLEG00000013662	3 retrocopies	retro_nleu_2505, retro_nleu_2737, retro_nleu_2864,
Oryctolagus cuniculus	ENSOCUG00000001888	2 retrocopies	retro_ocun_513, retro_ocun_728,
Otolemur garnettii	ENSOGAG00000003419	8 retrocopies	retro_ogar_2276, retro_ogar_2377, retro_ogar_2722, retro_ogar_3255, retro_ogar_3396, retro_ogar_755, retro_ogar_866, retro_ogar_885,
Ochotona princeps	ENSOPRG00000012582	1 retrocopy	retro_opri_404,
Pongo abelii	ENSPPYG00000014957	7 retrocopies	retro_pabe_1070, retro_pabe_1901, retro_pabe_2374, retro_pabe_3343, retro_pabe_3367, retro_pabe_592, retro_pabe_668,
Pan troglodytes	ENSPTRG00000016312	7 retrocopies	retro_ptro_1477, retro_ptro_1508, retro_ptro_2760, retro_ptro_2792, retro_ptro_441, retro_ptro_614, retro_ptro_884,
Rattus norvegicus	ENSRNOG00000010306	9 retrocopies	retro_rnor_1136, retro_rnor_1202, retro_rnor_1605, retro_rnor_1933, retro_rnor_2155, retro_rnor_2413, retro_rnor_2494, retro_rnor_2908, retro_rnor_788,
Ictidomys tridecemlineatus	ENSSTOG00000023194	1 retrocopy	retro_itri_1524,
Tupaia belangeri	ENSTBEG00000000478	15 retrocopies	retro_tbel_1289, retro_tbel_1290, retro_tbel_1320, retro_tbel_1925, retro_tbel_1959, retro_tbel_1972, retro_tbel_2304, retro_tbel_2526, retro_tbel_2685, retro_tbel_3575, retro_tbel_4077, retro_tbel_4308, retro_tbel_4369, retro_tbel_4451, retro_tbel_819,
Tarsius syrichta	ENSTSYG00000009462	2 retrocopies	retro_tsyr_1715, retro_tsyr_971,