RetrogeneDB ID: retro_fcat_39

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:105985075..105985720(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000023451
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCDC169
• Ensembl ID: ENSFCAG00000008786
• Aliases: None
• Description: coiled-coil domain containing 169 [Source:HGNC Symbol;Acc:34361]

Sequence

>retro_fcat_39
ATGGGGGACAGAAGAGGTGACAACTTCGAAAGTAGGGACACTGACTGCCTTAAATTGGAGTTAATGGAAGAAATCCACAT
GAGAGACTTAGTACAGCTTTCAATACTTGAATTAAGACAGGAGATAGTGAAACTGGAAGCCAAACTCAATACTGAAAATA
AAGGTGGTGAATGGAAAACACGTTATGAAGTCCAACTTGGACTGAATGATCATCTAGTAAAGCAAATTGCTACTCTCAAA
GAGAAAATGGAAAAACTCCGTGGAGATCCTTCAGATAGACTATCTTCTATTCGTGTCTATGAGCGAATGTCAGTGGAATC
CTTAAATACATTACTTAAACAGTTAGAAAAAGAAAAAAGGAGTCTTGAAAATCAAGTGAAAAATTGTGCACTTAGATTGG
AACAAGAGTCAAAGGCTTACCACAAAACCAGTGATGAATGCCGTGCATACCTAGCTGAAATGTCTCAGATCTCTAGCTCA
CACCAAGTTTCTAAAAGGCAACAGATGGATCAACTTCATAGAATGAAACAGAATCATGTGAAAACAGGAAGATGTAATCC
AACTAATCAGAAGATAGTAAATGCCAAGAAAGGACCAGCAAAAAAGATTACAAGATCAAACCATTTTCCAAAACTCAATC
TGTGA

Alignment

ORF - retro_fcat_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.95 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEGRGANFDGVSTDRLEKELLEEIHQKDIVQLSMLEIIHKIEELEAKLNTDDKGGEWKVRYETQLELND
          M...RG.NF....TD.L..EL.EEIH..D.VQLS.LE....I..LEAKLNT..KGGEWK.RYE.QL.LND
Retrocopy MGDRRGDNFESRDTDCLKLELMEEIHMRDLVQLSILELRQEIVKLEAKLNTENKGGEWKTRYEVQLGLND

Parental  QLEKQIVSLEEKMKKICGNPSDRLSFIRVYEKMPVESLNILLKQLEKEKRRLKNQVKDYALRLEQESKAY
          .L.KQI..L.EKM.K..G.PSDRLS.IRVYE.M.VESLN.LLKQLEKEKR.L.NQVK..ALRLEQESKAY
Retrocopy HLVKQIATLKEKMEKLRGDPSDRLSSIRVYERMSVESLNTLLKQLEKEKRSLENQVKNCALRLEQESKAY

Parental  HKTNNECHTYLAEMSQVSDSYQVSKRQQMDQLPRMKENSVKMVRYNPVNQKTMNAKRGPGKKITRSNHLP
          HKT..EC..YLAEMSQ.S.S.QVSKRQQMDQL.RMK.N.VK..R.NP.NQK..NAK.GP.KKITRSNH.P
Retrocopy HKTSDECRAYLAEMSQISSSHQVSKRQQMDQLHRMKQNHVKTGRCNPTNQKIVNAKKGPAKKITRSNHFP

Parental  KLD
          KL.
Retrocopy KLN

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	0.57 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_39 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_39 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004615	1 retrocopy	retro_amel_120,
Equus caballus	ENSECAG00000011446	1 retrocopy	retro_ecab_111,
Felis catus	ENSFCAG00000008786	1 retrocopy	retro_fcat_39 ,
Oryctolagus cuniculus	ENSOCUG00000026427	1 retrocopy	retro_ocun_406,
Otolemur garnettii	ENSOGAG00000010367	2 retrocopies	retro_ogar_1996, retro_ogar_957,
Sus scrofa	ENSSSCG00000026564	1 retrocopy	retro_sscr_77,