RetrogeneDB ID: retro_fcat_1827

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:71004577..71005360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B10
• Ensembl ID: ENSFCAG00000013899
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:HGNC Symbol;Acc:4800]

Sequence

>retro_fcat_1827
ATGGCTGCGGCATGTTGGAGCATGAAGGGCCTGGTTGCTCTAATAACCAGAGGAGCCTCTGGTCTAGGTCTGGCCACAGC
GGAGAGACTGACAGGACAAGGGACCACTGCTGTGCTTCTGGACCTGCCCAACGCTGATGGGGATGCCCAAGACAAGAAGT
TAGGGAAGAGCTGCGCCTTTGCCCCAGCTGACGTGACCTCGGAGAAGGACGTGAGAGCAGCTCTGACTGTAGCAAAAGAA
AAGTTTGGCCATGTGGATGCGGCAGTCAAATGTGCAGGCATTGCGGTGGCCATCAAGACATACAACCTAAAGAACAATCA
GGTCCACACCCTGGAGGACTCCCAGTGAGTTCTCAGTGTGAATCTCATGGGCACCTTCAATGTGATGCACCTGAGGTCTG
GTGAGATGGGCCTGGATGAACCAGACCAGGGAGGCCAACACGGTGTCATCATCAACACTGTCGGCATGGTTGCCTTTGAG
GGCCAGGCTGAATGAGCTGCTTCCTCTGCTTCCACAGGGGGCATAGTGGGCATGATGCTGCTCACTGCTCAGTGTCCGGC
TCCCATGGGCATCCGAGTGGTGACCACTGCTCCCGGCCTACTTGGCACTCTGCTGCCGACCAGCCTCCCAGAAAAACTAT
GCGACTTCTTGGCCAGCCAAGCGCCCCTCCCCAGCAGACTGGGTAGTCTCGCCGAGTATGCTCATCTGGTATAAGCTGTC
GTGGAGAACCCATTCATCAGTGGAGAGGTCATCCCGCTGGGTGGGGCCATCTGCATGCAGCCT

Alignment

ORF - retro_fcat_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAACRTVKGLVALITGGASGLGLATAERLVGQGATAVLLDLPNSDGEVQAKKLGKSCVFAPADVTSEKD
          MAAAC...KGLVALIT.GASGLGLATAERL.GQG.TAVLLDLPN.DG..Q.KKLGKSC.FAPADVTSEKD
Retrocopy MAAACWSMKGLVALITRGASGLGLATAERLTGQGTTAVLLDLPNADGDAQDKKLGKSCAFAPADVTSEKD

Parental  VQAALTLAREKFGRVDVAVNCAGIAVAMKTYNLKKNQAHTLEDFQRVLNVNLMGTFNVIRLVAGEMGQNE
          V.AALT.A.EKFG.VD.AV.CAGIAVA.KTYNLK.NQ.HTLED.Q.VL.VNLMGTFNV..L..GEMG..E
Retrocopy VRAALTVAKEKFGHVDAAVKCAGIAVAIKTYNLKNNQVHTLEDSQ*VLSVNLMGTFNVMHLRSGEMGLDE

Parental  PDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPMGIRVMTIAPGLFGTPLLTSLP
          PDQGGQ.GVIINT....AFEGQ...AA.SAS.GGIVGM.L..A...APMGIRV.T.APGL.GT.L.TSLP
Retrocopy PDQGGQHGVIINTVGMVAFEGQAE*AASSASTGGIVGMMLLTAQCPAPMGIRVVTTAPGLLGTLLPTSLP

Parental  EKVRNFLASQVPFPSRLGDPAEYAHLVQAIIENPFINGEVIRLDGAIRMQP
          EK...FLASQ.P.PSRLG..AEYAHLV.A..ENPFI.GEVI.L.GAI.MQP
Retrocopy EKLCDFLASQAPLPSRLGSLAEYAHLV*AVVENPFISGEVIPLGGAICMQP

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	16.30 RPM
SRP017611_kidney	0.00 RPM	50.50 RPM
SRP017611_liver	0.00 RPM	27.09 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1827 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1827 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.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827 ,
Felis catus	ENSFCAG00000030280	1 retrocopy	retro_fcat_885,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,