RetrogeneDB ID: retro_cfam_2171

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:62762523..62762914(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LEPROTL1
• Ensembl ID: ENSCAFG00000006530
• Aliases: None
• Description: leptin receptor overlapping transcript-like 1 [Source:HGNC Symbol;Acc:6555]

Sequence

>retro_cfam_2171
GCAGGCATCAAAGCATTGATTAGTTTGTCCTTTGGAGGAGCAATTGGGCTTATGTTTTTGATGCTTGGATGTGCCCTTCC
AATATACAACCAATACTGGCCTCTCTTTGTTCTGTTGTTTTACATCCTTTCACCTGTTCCATTCTGCATAGCGAAAAGAT
TAGTGGAAGACATAGATGCTATGAATAACACTTGTAAGGAACTTGCCATATTTCTTACAGCAAGCATTGTTGTCTCAGCT
TTTGGACTCCCTGTTGTGTTTGCCAGAGCACATCTGATTGAGTGGGGAGCTTGTGCACTTATTCTGAACAGGAAACACAG
TCATCTTTGCAACTACACTGGGCTTTTTCTTGGTCTTTGGAAGCAATGATTACTTCAGCTGGCAGCAGTGG

Alignment

ORF - retro_cfam_2171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.02 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGIPALISLSFGGAIGLMFLMLGCALPIYNQYWPLFVLFFYILSPIPYCIARRLVDDTDAMSNACKELAI
          .GI.ALISLSFGGAIGLMFLMLGCALPIYNQYWPLFVL.FYILSP.P.CIA.RLV.D.DAM.N.CKELAI
Retrocopy AGIKALISLSFGGAIGLMFLMLGCALPIYNQYWPLFVLLFYILSPVPFCIAKRLVEDIDAMNNTCKELAI

Parental  FLTTGIVVSAFGLPIVFARAHLIEWGACALVL-TGNTVIFATILGFFLVFGSNDDFSWQQW
          FLT..IVVSAFGLP.VFARAHLIEWGACAL.L.TGNTVIFAT.LGFFLVFGSND.FSWQQW
Retrocopy FLTASIVVSAFGLPVVFARAHLIEWGACALIL>TGNTVIFATTLGFFLVFGSNDYFSWQQW

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	19.24 RPM
SRP017611_brain	0.00 RPM	13.26 RPM
SRP017611_kidney	0.00 RPM	23.18 RPM
SRP017611_liver	0.00 RPM	10.51 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2171 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2171 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	ENSCAFG00000006530	1 retrocopy	retro_cfam_2171 ,
Choloepus hoffmanni	ENSCHOG00000012299	1 retrocopy	retro_chof_1305,
Dasypus novemcinctus	ENSDNOG00000014538	3 retrocopies	retro_dnov_1528, retro_dnov_2606, retro_dnov_876,
Erinaceus europaeus	ENSEEUG00000001360	1 retrocopy	retro_eeur_139,
Oryctolagus cuniculus	ENSOCUG00000013931	1 retrocopy	retro_ocun_832,