RetrogeneDB ID: retro_fcat_1400

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:61053329..61053584(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSFCAG00000028793
• Aliases: None
• Description: high mobility group nucleosomal binding domain 3 [Source:HGNC Symbol;Acc:12312]

Sequence

>retro_fcat_1400
GGCAAGGACGGATCCAAACCAACTGAACAGGAGACCACCAGACAGTCTGCCAGATTGTCAGCGAAACCCACTCCACCAAA
AGCTGAATCTAAACCAAGGAAAACATCTGCGAACAAAGAACCTGGCACAAAGACTAACAAAGGTACTAAAGGGAAAGAGG
GAGAGCAAGAAGCTGAAAAGGAAGATACCGCGCCATTTCCAAATGGTGAAACTAAAGCTGAAAAGGCGCGGAAAGCTGAA
CCTGTAGATCACAGG

Alignment

ORF - retro_fcat_1400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.09 %
• Parental protein coverage: 86.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKDGSKVTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGTKINKGAKGKKEEKQEAGKEGTAPSEKG
          GKDGSK.T.QE.TR.SARLSAKP.PPK.E.KPRKTSA.KEPGTK.NKG.KG.KE..QEA.KE.TAP...G
Retrocopy GKDGSKPTEQETTRQSARLSAKPTPPKAESKPRKTSANKEPGTKTNKGTKG-KEGEQEAEKEDTAPFPNG

Parental  ETKAEEAQKTESVDNK
          ETKAE.A.K.E.VD..
Retrocopy ETKAEKARKAEPVDHR

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
SRP017611_brain	0.00 RPM	20.54 RPM
SRP017611_kidney	0.00 RPM	19.48 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1400 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Cavia porcellus	ENSCPOG00000012407	2 retrocopies	retro_cpor_1399, retro_cpor_147,
Felis catus	ENSFCAG00000028793	1 retrocopy	retro_fcat_1400 ,
Homo sapiens	ENSG00000118418	1 retrocopy	retro_hsap_231,
Gorilla gorilla	ENSGGOG00000006910	1 retrocopy	retro_ggor_293,
Macaca mulatta	ENSMMUG00000004351	1 retrocopy	retro_mmul_414,
Nomascus leucogenys	ENSNLEG00000012377	2 retrocopies	retro_nleu_68, retro_nleu_851,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Ochotona princeps	ENSOPRG00000009611	1 retrocopy	retro_opri_799,
Pan troglodytes	ENSPTRG00000018366	2 retrocopies	retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus	ENSSTOG00000014353	1 retrocopy	retro_itri_251,
Tupaia belangeri	ENSTBEG00000015468	3 retrocopies	retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta	ENSTSYG00000005238	3 retrocopies	retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,