RetrogeneDB ID: retro_cfam_1658

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:48937545..48938063(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAF1
• Ensembl ID: ENSCAFG00000006017
• Aliases: None
• Description: ELL associated factor 1 [Source:HGNC Symbol;Acc:20907]

Sequence

>retro_cfam_1658
GTGCTGGAAAAACTCAGCAGCAGCATTCAGGTCAAGAAAACAAGAGCCAAGGGGAGCAGTAAAATCCAAGCCCGAATGGA
ACAGCAGCCCCCTCGTCCCCCGCAGCCATCACAGCCACCACCACCTCCACCAGCTATGCCATTCAGAGCTCCAGCAAAGC
CTCCAGTTGGACCCAAAACTTCCCCCTTGAAAGCTAACCCCTCACCTGAACCCCAGCCGGATGACATCAAAGGAGAGCTG
AGGGCCGAAGCTGACACTTTGAACAGAGGAGCGGCAGCAGCGGGAGCAGGTCCTCAGACTCCGAGCGCCCATCAGGAAGC
GAAGACGACAGCTCGAGCAGCGGGGCTGGGGACAATGGCCCAGCGCCCCCTCGGCCGCCCGCGCCCGCACACCAGCAGCC
CTGCACCAGCAGGCCGGCCGTGGCCAACGGAACCAGCCGGCCGCAAGGAAGCAACCAGCTCATGAACACGCTCAGAAATG
ACTGGCAGTTGAGCGAGTCCGGCAGTGACAGTGATGAC

Alignment

ORF - retro_cfam_1658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.06 %
• Parental protein coverage: 63.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLEKLSSSIQVKKTRAEGSSKIQARMEQQPTRPPQPSQPPPPPPPMPFRAPTKPPVGPKTSPLKDNPSPE
          VLEKLSSSIQVKKTRA.GSSKIQARMEQQP.RPPQPSQPPPPPP.MPFRAP.KPPVGPKTSPLK.NPSPE
Retrocopy VLEKLSSSIQVKKTRAKGSSKIQARMEQQPPRPPQPSQPPPPPPAMPFRAPAKPPVGPKTSPLKANPSPE

Parental  PQLDDIKRELRAEVDII-EQMSSSSGSSSSDSESSSGSDDDSSSSGGEDNGPA--SPPLPAHQQPYNSRP
          PQ.DDIK.ELRAE.D...EQ.S.SSGS.SSDSE..SGS.DDSSSSG..DNGPA...PP.PAHQQP..SRP
Retrocopy PQPDDIKGELRAEADTL<EQRSGSSGSRSSDSERPSGSEDDSSSSGAGDNGPAPPRPPAPAHQQPCTSRP

Parental  AVANGTSRPQGSNQLMNTLRNDLQLSESGSDSDD
          AVANGTSRPQGSNQLMNTLRND.QLSESGSDSDD
Retrocopy AVANGTSRPQGSNQLMNTLRNDWQLSESGSDSDD

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	17.51 RPM
SRP017611_brain	0.00 RPM	12.23 RPM
SRP017611_kidney	0.00 RPM	18.82 RPM
SRP017611_liver	0.00 RPM	5.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1658 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1658 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006017	1 retrocopy	retro_cfam_1658 ,
Choloepus hoffmanni	ENSCHOG00000007449	4 retrocopies	retro_chof_1039, retro_chof_2342, retro_chof_355, retro_chof_883,
Erinaceus europaeus	ENSEEUG00000002084	1 retrocopy	retro_eeur_254,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Otolemur garnettii	ENSOGAG00000013964	1 retrocopy	retro_ogar_2142,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56,