RetrogeneDB ID: retro_cfam_1907

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:29111183..29111602(+)
• Located in intron of: ENSCAFG00000014843

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_1907
GACACCTGTAGTTCCTTAGCAAAAGATGTTAACCTATGTCTACATATCCTGAGCCTTCCCAATGGGATCTCATTCCCTTG
TACTATGCATCACCCAGTACCAGAAAAAGATATTTGAAATATGAAAATTACTCAGCCTCAGAAAGACTGTCTTTCTGAAA
AGAGGGCTGAGTTGTATAGAGGCCGAAGACCAAGAACTGCTTTTAGTCAAAACCAGACTGAAGTGTTGGAAAATGTCTTT
ACAGTAAATGCTATGAGTAATGCTGGTATTAATACTGGAGAAGACTTCGCTCAAAACTGAATCTAGAACAAGACAGAATC
CAAATCTGTTTCCAAAATCAGCATGCACAGCTGAAAAAATCCCATAGAGAATCGCTGTTTTCAATGGTGAAAACAAATTT
CAATACAAATCTCCTGGAA

Alignment

ORF - retro_cfam_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 75.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DTCGSSGKDVNLCVHIPSLPNGISLPCTVDHPMPEE-KFLKYENYFSASERLSLKRE-LSWYRGRRPRTA
          DTC.S..KDVNLC.HI.SLPNGIS.PCT..HP.PE....LKYENY.SASERLS...E....YRGRRPRTA
Retrocopy DTCSSLAKDVNLCLHILSLPNGISFPCTMHHPVPEK<RYLKYENY-SASERLSF*KE>AELYRGRRPRTA

Parental  FTQNQIEVLENVFRVNCYP--GIDIREDLAR-KLNLEEDRIQIWFQNRRAKLKRSHRESQFLMAKKNFNS
          F.QNQ.EVLENVF.VN.....GI...ED.A..KLNLE.DRIQI.FQN..A.LK.SHRES.F.M.K.NFN.
Retrocopy FSQNQTEVLENVFTVNAMSNAGINTGEDFAQ<KLNLEQDRIQICFQNQHAQLKKSHRESLFSMVKTNFNT

Parental  NLLE
          NLLE
Retrocopy NLLE

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	0.08 RPM	0.00 RPM
SRP017611_kidney	0.13 RPM	0.00 RPM
SRP017611_liver	0.07 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1907 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1907 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,