RetrogeneDB ID: retro_cfam_27

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:16650316..16650970(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004924
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBE2E3
• Ensembl ID: ENSCAFG00000014163
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 3 [Source:HGNC Symbol;Acc:12479]

Sequence

>retro_cfam_27
GGAGGCAGAACTGGAACAGCCGCGGGTGGAGGCAGCAGCGCTGAGGGATCTAACATGTCCACTGAGGCACAAAGAGTTGA
TGACAGTCCAAGCACTAGTGGAGGAAGTTCTGATGGAGACCAACGTGAAAGTGTTCAACAAGAACCAGAAAGAGAACAAG
TTCAGCCCAAGAAAAAGGAAGGAAAAATATCCAGCAAAACAGCTGCTAAATTGACGAGTGCTAAAAGAATTCAGAAGGAA
CTTGCAGAGATTACATTGGACCCTCCTCCCAACTGTAGTGCTGGACCCAAAGGAGACAACATTTATGAATGGAGGTCAAC
TATATTGGGACCCCCAGGATCTGTCTATGAGGGAGAGGCGTTCTTTCTTGACATTACCTTTTCACCAGACTATCCTTTTA
AACCCCCTAAGGTTACCTTCCGAACAAGAATCTATCACTGTAATATTAACAGCCAGGATGTCATCTGTCTGGATATCCTA
AAGGATAACTGGAGTCCAGCCCTAACCATTTCTAAAGTTCTCCTCTCCATCTGCTCACTTCTTACAGATTGCAACCCTGC
TGACCCTCTAGTGGGTAGCATTGCCACACAGTACATTACCAACAGAGCAGAGCATGACCAGATGGCCAGACAGTGGACCA
AGCAGTATGCCACA

Alignment

ORF - retro_cfam_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKEL
          MS...QR.DD.SPSTS.GSSD.DQR.....EPE..E...P.....KK..K.SSKT.AKL.TSAKRIQKEL
Retrocopy MSTEAQRVDD-SPSTSGGSSDGDQRESVQQEPE-REQVQP----KKKEGKISSKTAAKL-TSAKRIQKEL

Parental  AEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSDYPFKPPKVTFRTRIYHCNINS
          AEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEG..FFLDITFS.DYPFKPPKVTFRTRIYHCNINS
Retrocopy AEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGEAFFLDITFSPDYPFKPPKVTFRTRIYHCNINS

Parental  QGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYAT
          Q.VICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQY.TNRAEHD..ARQWTK.YAT
Retrocopy QDVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYITNRAEHDQMARQWTKQYAT

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	6.89 RPM	159.30 RPM
SRP017611_brain	3.49 RPM	61.53 RPM
SRP017611_kidney	1.52 RPM	54.08 RPM
SRP017611_liver	1.23 RPM	20.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_27 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_27 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27 ,
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090,
Canis familiaris	ENSCAFG00000031041	5 retrocopies	retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,