RetrogeneDB ID: retro_cfam_2150

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:40254370..40255413(-)
• Located in intron of: ENSCAFG00000014767

Retrocopy information

• Ensembl ID: ENSCAFG00000014790
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BZW1
• Ensembl ID: ENSCAFG00000011878
• Aliases: None
• Description: basic leucine zipper and W2 domains 1 [Source:HGNC Symbol;Acc:18380]

Sequence

>retro_cfam_2150
GACATTCTGGTGGCCGGCGGAATGCTGGCCCCAGGGGGTACACTGGCAGATGACATGATGCGTACAGATGTCTGTGTGTT
CGCAGCACAAGAAGACCTAGAGACCATGCAAGCATTTGCTCAGGTTTTTAACAAGTTAATCAGGCGCTACAAATACCTGG
AGAAAGGTTTTGAAGATGAAGTAAAAAAGCTGCTGCTGTTCTTAAAGGGTTTTTCAGAGTCGGAGAGGAACAAGCTGGCT
ATGTTGACTGGTGTTCTTCTGGCTAATGGAACACTTAATGCATCCATTCTTAATAGCCTTTATAATGAGAATTTGGTTAA
AGAAGGGGTTTCAGCAGCTTTTGCTGTAAAGCTCTTTAAATCATGGATAAATGAAAAAGATATCAATGCAGTAGCTGCAA
GTCTTCGGAAAGTCAGCATGGATAACAGACTGATGGAACTTTTTCCTGCCAATAAACAAAGCGTTGAACACTTCACAAAG
TATTTTACTGAGGCAGGCTTGAAAGAACTTTCAGAATATGTTCGGAATCAACAAACCATAGGAGCTCGAAAGAACTCCAG
AAAGAACTTCAAGAACAGATGTCCTGTGATGATCCATTTAAGGATATAATTTTGTATGTCAAGGAGGAGATGAAAAAAAA
CAACATCCCAGAAACCGTTGTCATTGGAATAGTCTGGTCCAGCGTAATGAGCACCGTGGAATGGAACAAAAAGGAGGAGC
TTGTAGCAGAGCAAGCCATCAAGCACTTGAAGCAATACAGCCCTCTACTTGCTGCCTTTACTACTCAAGGTCAGTCTGAG
CTGACTCTGTTATTGAAGATTCAGGAGAATTGCTATGACAACATTCATTTCATGAAAGCCTTCCAGAAAATAGTGGTGCT
TTTTTATAAAGCTGAAGTCCTGAGTGAAGAGCCCATTCTGAAGTGGTATAAAGATGCACATGTTGCCAAGGGGAAAAGCG
TCTTCCTTAAGCAAATGAAAAAGTTTGTAGAGTGGCTCAAAAATGCTGAAGAAGAATCTGAGTCTGAAGCTGAAGAAGGT
GAC

Alignment

ORF - retro_cfam_2150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 77.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DILVAGGMLAPGGTLADDMMRTDVCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFLKG
          DILVAGGMLAPGGTLADDMMRTDVCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFLKG
Retrocopy DILVAGGMLAPGGTLADDMMRTDVCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFLKG

Parental  FSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSM
          FSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSM
Retrocopy FSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSM

Parental  DNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARK-ELQKELQEQMSRGDPFKDIILYVKE
          DNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARK.ELQKELQEQMS..DPFKDIILYVKE
Retrocopy DNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARK<ELQKELQEQMSCDDPFKDIILYVKE

Parental  EMKKNNIPEPVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCY
          EM...NIPE.VVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQE.CY
Retrocopy EMXXXNIPETVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQENCY

Parental  DNIHFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD
          DNIHFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFL.QMKKFVEWLKNAEEESESEAEEGD
Retrocopy DNIHFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLKQMKKFVEWLKNAEEESESEAEEGD

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	0.04 RPM	92.78 RPM
SRP017611_brain	2.54 RPM	70.74 RPM
SRP017611_kidney	6.08 RPM	141.25 RPM
SRP017611_liver	1.74 RPM	51.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2150 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011878	1 retrocopy	retro_cfam_2150 ,
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus	ENSCPOG00000010449	1 retrocopy	retro_cpor_331,
Homo sapiens	ENSG00000082153	2 retrocopies	retro_hsap_2832, retro_hsap_2881,
Gorilla gorilla	ENSGGOG00000016296	1 retrocopy	retro_ggor_1997,
Mustela putorius furo	ENSMPUG00000012344	1 retrocopy	retro_mputfur_1174,
Mus musculus	ENSMUSG00000051223	3 retrocopies	retro_mmus_2499, retro_mmus_751, retro_mmus_990,
Nomascus leucogenys	ENSNLEG00000006929	1 retrocopy	retro_nleu_621,
Pan troglodytes	ENSPTRG00000012791	1 retrocopy	retro_ptro_1949,