RetrogeneDB ID: retro_cfam_480

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:16125674..16126748(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002101
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSDL2
• Ensembl ID: ENSCAFG00000003028
• Aliases: None
• Description: Canis lupus familiaris hydroxysteroid dehydrogenase like 2 (HSDL2), mRNA. [Source:RefSeq mRNA;Acc:NM_001199130]

Sequence

>retro_cfam_480
GTTGAAGCAGCTGGAGGAAAGGCCTTGCCATGTTCTGTTGATGTGAGAGATGAACAGCAAATCAGTAATGCAGTGGAGAA
AGCAGTGGAGCGATTTGGAGGAATTGATATTTTGGTGAATAATGCCAGTGCTATTAGCTTGACCAATACATTGGAAACAC
CTACGAAGAGAGTCGATTTGATGATGAATGTCAACACCAGAGGCACCTATCTGACATCTAAAGCATGCATTCCTTATTTG
AAAAAGAGTAAAATTGCTCATATCCTCAATCTCAGCCCACCACTGAACTTAAATCCAATGTGGTTCAAACAGCACTGTGC
TTATACCATTGCTAAGTATGGTATGTCTATGTGTGTGCTTGGGATGGCAGAAGAATTTAAGGGTGAAATTGCAGTCAATG
CATTATGGCCTAAAACAGCCATCCACACCGCTGCTATGGATATGCTGGGAGGATCTGGTATTGAAAGCCAGTGTAGAAAA
GTTGAGATCATTGCCGATGCTGCCTATTCCATTTTTAAAAGGCCAAAAAGTTTTACTGGAAACTTTATTATTGATGAAAA
TATCTTAAGAGAAGAAGGAATAAAAAATTTTGACATCTATGCAATTAAACCAGGCCATCCCTTGTTACCAGATTTCTTCT
TAGATGAACACCCAGATATAATTATCAAGAAAGCGGAATCACGTGATGTTATTCCGGAATTGAAAGAAGAGAAGCCACAG
CCACCACCAAAACAACGTTCTGGAGCTGTGGAAGAAACATTTAGAATTGTTAAGGACTCTCTTAGTGATGACATTGTTAA
AGCCACTCAAGCAGTTTATCAGTTTGAACTCTCAGGTGAAGATGGTGGAACGTGGTTTCTTGATCTTAAAAGCAAAGGTG
GGAATGTCGGATATGGAGAGCCCTCCAATCAGGCGGATGTGGTGATGAGTATGTCTACTGATGATTTTGTAAAAATGTTT
TCAGGAAAACTAAAACCAACAATGGCATTCATGTCAGGAAAATTGAAGATTAAAGGAAACATGGCCCTAGCAATCAAATT
GGAGAAGCTAATGAATCAGATGAATGCCAAGCTG

Alignment

ORF - retro_cfam_480 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.72 %
• Parental protein coverage: 85.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEAAGGKALPCSVDVRDEQQISNAVEKAVERFGGIDILVNNASAISLTNTLETPTKRVDLMMNVNTRGTY
          .EAAGGKALPCSVDVRDEQQISNAVEKAVERFGGIDILVNNASAISLTNTLETPTKRVDLMMNVNTRGTY
Retrocopy VEAAGGKALPCSVDVRDEQQISNAVEKAVERFGGIDILVNNASAISLTNTLETPTKRVDLMMNVNTRGTY

Parental  LTSKACIPYLKKSKIAHILNLSPPLNLNPMWFKQHCAYTIAKYGMSMCVLGMAEEFKGEIAVNALWPKTA
          LTSKACIPYLKKSKIAHILNLSPPLNLNPMWFKQHCAYTIAKYGMSMCVLGMAEEFKGEIAVNALWPKTA
Retrocopy LTSKACIPYLKKSKIAHILNLSPPLNLNPMWFKQHCAYTIAKYGMSMCVLGMAEEFKGEIAVNALWPKTA

Parental  IHTAAMDMLGGSGIESQCRKVEIIADAAYSIFKRPKSFTGNFIIDENILREEGIKNFDIYAIKPGHPLLP
          IHTAAMDMLGGSGIESQCRKVEIIADAAYSIFKRPKSFTGNFIIDENILREEGIKNFDIYAIKPGHPLLP
Retrocopy IHTAAMDMLGGSGIESQCRKVEIIADAAYSIFKRPKSFTGNFIIDENILREEGIKNFDIYAIKPGHPLLP

Parental  DFFLDEHPDIIIKKAESRDVIPELKEEKPQPPPKQRSGAVEETFRIVKDSLSDDIVKATQAVYQFELSGE
          DFFLDEHPDIIIKKAESRDVIPELKEEKPQPPPKQRSGAVEETFRIVKDSLSDDIVKATQAVYQFELSGE
Retrocopy DFFLDEHPDIIIKKAESRDVIPELKEEKPQPPPKQRSGAVEETFRIVKDSLSDDIVKATQAVYQFELSGE

Parental  DGGTWFLDLKSKGGNVGYGEPSNQADVVMSMSTDDFVKMFSGKLKPTMAFMSGKLKIKGNMALAIKLEKL
          DGGTWFLDLKSKGGNVGYGEPSNQADVVMSMSTDDFVKMFSGKLKPTMAFMSGKLKIKGNMALAIKLEKL
Retrocopy DGGTWFLDLKSKGGNVGYGEPSNQADVVMSMSTDDFVKMFSGKLKPTMAFMSGKLKIKGNMALAIKLEKL

Parental  MNQMNAKL
          MNQMNAKL
Retrocopy MNQMNAKL

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	9.16 RPM	26.00 RPM
SRP017611_brain	5.88 RPM	17.55 RPM
SRP017611_kidney	28.53 RPM	107.90 RPM
SRP017611_liver	14.29 RPM	84.26 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_480 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DN379289	16125587	16126142	99.9	553	1	552

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_480 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006832	1 retrocopy	retro_amel_1368,
Canis familiaris	ENSCAFG00000003028	1 retrocopy	retro_cfam_480 ,
Nomascus leucogenys	ENSNLEG00000016534	1 retrocopy	retro_nleu_649,
Ictidomys tridecemlineatus	ENSSTOG00000012222	1 retrocopy	retro_itri_471,
Tupaia belangeri	ENSTBEG00000013420	2 retrocopies	retro_tbel_2324, retro_tbel_3321,