RetrogeneDB ID: retro_cfam_870

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:23937801..23938794(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004629
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CRYZ
• Ensembl ID: ENSCAFG00000020404
• Aliases: None
• Description: Canis lupus familiaris crystallin, zeta (quinone reductase) (CRYZ), mRNA. [Source:RefSeq mRNA;Acc:NM_001252397]

Sequence

>retro_cfam_870
ATCACCATGGCGACTGCAGGGAAGTTGATGAGAGCGATTCGGGTTTTTGAATTTGGTGGACCAGAAGTGCTGAAACTCCG
GTCGGATGTTGCGGTACCAATTCCAAAAGACCATCAGGTTCTGATCAAAGTCCACGCATGTGGTGTAAACCCCGTGGAAA
CATATATTCGGTCTGGTACTTACAGAAGAAAACCACTCTTACCCTACACGCCGGGTTCAGACGTGGCTGGGATAATAGAA
GCTATTGGAGAGAATGTATCTACTTTCAAGAAAGGTGACAGAGTTTTCACTACCGCCACCATCTCTGGGGGCTATGCTGA
GTATGCCCTTGCTTCAGATCACACTGTGTACATACTGCCGGAGAAACTGGACTTGAAACAAGGAGCTGCCATCGGCATCC
CGTATTTTACTGCATACCGAGCTCTGCTCCACAGCGCCCGCGCGAAAGCCGGAGAAAGTGTTCTGGTTCATGGGGCTAGT
GGAGGAGTTGGAATAGCAGCGTGCCAGATTGCCAGGGCTTACGGCCTAAAAGTTTTAGGTACGGCTGGTACCGAGGAAGG
ACAAAACATTGTCTTGCAGAATGGAGCCCATGAAGTGTTTAATCACAGAGAACTTAATTATATTGATAAAATCAAGAAAT
CTGTTGGTGAAAAAGGCATTGATGTGATCATTGAAATGCTAGCTAATGTAAATCTGAGTAATGATTTGGATCTTCTGTCG
TATGGAGGACGAGTAATAGTTGTTGGCAGCAGAGGTCCTATTGAAATAAACCCACGGGACACCATCCCAAAGGAAACCAG
TATAATTGGAACTGCTCTTTATTCATCAACTAAGGAGGAATTTAGGAAATTTGCAATGGCCCTTCAAGCTGGAATGGAAA
TCGGTTGGTTGAAACCTGTGATAGGTCCTCAGTATTCACTGGAGAAGGTGGTCCAGGCTCACGAAAATATCATCCACAGC
AGTGGGGCTATTGGGAAAATGATTCTTCTCTTA

Alignment

ORF - retro_cfam_870 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 98.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITMATAGKLMRAIRVFEFGGPEVLKLRSDVAVPIPKDHQVLIKVHACGVNPVETYIRSGTYRRKPLLPYT
          ITMATAGKLMRAIRVFEFGGPEVLKLRSDVAVPIPKDHQVLIKVHACGVNPVETYIRSGTYRRKPLLPYT
Retrocopy ITMATAGKLMRAIRVFEFGGPEVLKLRSDVAVPIPKDHQVLIKVHACGVNPVETYIRSGTYRRKPLLPYT

Parental  PGSDVAGIIEAIGENVSTFKKGDRVFTTATISGGYAEYALASDHTVYILPEKLDLKQGAAIGIPYFTAYR
          PGSDVAGIIEAIGENVSTFKKGDRVFTTATISGGYAEYALASDHTVYILPEKLDLKQGAAIGIPYFTAYR
Retrocopy PGSDVAGIIEAIGENVSTFKKGDRVFTTATISGGYAEYALASDHTVYILPEKLDLKQGAAIGIPYFTAYR

Parental  ALLHSARAKAGESVLVHGASGGVGIAACQIARAYGLKVLGTAGTEEGQNIVLQNGAHEVFNHRELNYIDK
          ALLHSARAKAGESVLVHGASGGVGIAACQIARAYGLKVLGTAGTEEGQNIVLQNGAHEVFNHRELNYIDK
Retrocopy ALLHSARAKAGESVLVHGASGGVGIAACQIARAYGLKVLGTAGTEEGQNIVLQNGAHEVFNHRELNYIDK

Parental  IKKSVGEKGIDVIIEMLANVNLSNDLDLLSYGGRVIVVGSRGPIEINPRDTIPKETSIIGTALYSSTKEE
          IKKSVGEKGIDVIIEMLANVNLSNDLDLLSYGGRVIVVGSRGPIEINPRDTIPKETSIIGTALYSSTKEE
Retrocopy IKKSVGEKGIDVIIEMLANVNLSNDLDLLSYGGRVIVVGSRGPIEINPRDTIPKETSIIGTALYSSTKEE

Parental  FRKFAMALQAGMEIGWLKPVIGPQYSLEKVVQAHENIIHSSGAIGKMILLL
          FRKFAMALQAGMEIGWLKPVIGPQYSLEKVVQAHENIIHSSGAIGKMILLL
Retrocopy FRKFAMALQAGMEIGWLKPVIGPQYSLEKVVQAHENIIHSSGAIGKMILLL

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	1.26 RPM	5.92 RPM
SRP017611_brain	0.87 RPM	8.34 RPM
SRP017611_kidney	2.97 RPM	39.03 RPM
SRP017611_liver	2.68 RPM	44.60 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_870 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_870 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870 ,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,