RetrogeneDB ID: retro_cfam_954

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:1439879..1440434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HESX1
• Ensembl ID: ENSCAFG00000007995
• Aliases: None
• Description: HESX homeobox 1 [Source:HGNC Symbol;Acc:4877]

Sequence

>retro_cfam_954
ATGGTTCCCAGTCTTCAGGAGGATGCTCAGCTTGGGGAACGCAAACCCTCATCCTGCTCCTTTTCGATTGAGAGCATTTT
AGGATTGGACCAAAAGAAAGACTGTATTCCTTCGATGAAACCCCACAGGCCCTGAGCAGACACCTGCGGCTCCTCAGGGA
AAGATGTTAACCTCTGCGTTCATATCCAAAGCCTTCTTAATGGGATCTCATTCCCTTGTACTGTGGATCACCCAATGCCA
GAAGAGAAATTTTTGAAATACGAAAATTACTTTTCGGCCTCAGAAAGGCTGTCTTTGAAAAGAGAACTGAGCTGATATAG
GGGCCGGAGACCCAGAACTGCTTTTACTCAAAACCAGATTGAAGTGTTGGAAAATGTCTTTAGAGTAAACTGCTATCCCG
GCATTGATATCAGAGAAGACTTAGCTTGGAAATTGAATCTAGAGGAAGACACAATCCAGATCTGATTCCAAAATCGGCAT
GCAAAGCTGAAAAGGTCCCACAGAGAATCACAGTTTCTAATGGTGAAAAAAAAATTCAACTCAAATCTCCTGGAA

Alignment

ORF - retro_cfam_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPSLQEGAQLGERKPSSCSFSIESILGLDQKKDCIPSMKPHRPWADTCGSSGKDVNLCVHIPSLPNGIS
          M.PSLQE.AQLGERKPSSCSFSIESILGLDQKKDCIPSMKPHRP.ADTCGSSGKDVNLCVHI.SL.NGIS
Retrocopy MVPSLQEDAQLGERKPSSCSFSIESILGLDQKKDCIPSMKPHRP*ADTCGSSGKDVNLCVHIQSLLNGIS

Parental  LPCTVDHPMPEEKFLKYENYFSASERLSLKRELSWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIRED
          .PCTVDHPMPEEKFLKYENYFSASERLSLKRELS.YRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIRED
Retrocopy FPCTVDHPMPEEKFLKYENYFSASERLSLKRELS*YRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIRED

Parental  LARKLNLEEDRIQIWFQNRRAKLKRSHRESQFLMAKKNFNSNLLE
          LA.KLNLEED.IQI.FQNR.AKLKRSHRESQFLM....FNSNLLE
Retrocopy LAWKLNLEEDTIQI*FQNRHAKLKRSHRESQFLMVXXXFNSNLLE

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	0.08 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_954 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_954 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007995	2 retrocopies	retro_cfam_1907, retro_cfam_954 ,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Mustela putorius furo	ENSMPUG00000016854	2 retrocopies	retro_mputfur_112, retro_mputfur_174,
Tupaia belangeri	ENSTBEG00000017505	1 retrocopy	retro_tbel_339,