RetrogeneDB ID: retro_cfam_958

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:19955795..19956117(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB2
• Ensembl ID: ENSCAFG00000003930
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7697]

Sequence

>retro_cfam_958
GCTAGCATGTCGGCTCTGATGCGCTTGGCGTCTTTGGTTCACGTTGGAGGCCAGTTGTTCAGAGGCCCCGGCCAGCAGGC
GGCTGGAGGCGGTGGAGTCCATCATGCTGGTGGCAAGGTGCATATTGAGCCCCGGTGTAGACAGCTTCCCCAGCTGACCA
GGTCCCAGATGATCCAGGCCGAGTTCTTCAGTGGCACCATGTGGTTCTGGATTCTCTGGCATTTTTTGGCATGACTCAGA
TGCTGTGCTGGGTCACTTTCCATATCCAGATCCTTCCCAGTGGATGGATGAGAAACTAGGTATCCTTCCTGATGATGAAG
AC

Alignment

ORF - retro_cfam_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGMSALTRLAPFVRVGGQLFRGPGPRAAGGGGVRHAGGDVHIEPRYRQFPQLTRSQVIQAEFFSGTMWFW
          A.MSAL.RLA..V.VGGQLFRGPG..AAGGGGV.HAGG.VHIEPR.RQ.PQLTRSQ.IQAEFFSGTMWFW
Retrocopy ASMSALMRLASLVHVGGQLFRGPGQQAAGGGGVHHAGGKVHIEPRCRQLPQLTRSQMIQAEFFSGTMWFW

Parental  ILWR-FWHDSDAVLGHFPYPDPSQWTDEELGILPDDED
          ILW..FWHDSDAVLGHFPYPDPSQW.DE.LGILPDDED
Retrocopy ILWH>FWHDSDAVLGHFPYPDPSQWMDEKLGILPDDED

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	0.76 RPM	47.33 RPM
SRP017611_brain	0.16 RPM	23.90 RPM
SRP017611_kidney	1.52 RPM	107.97 RPM
SRP017611_liver	0.22 RPM	21.83 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_958 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_958 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958 ,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,