RetrogeneDB ID: retro_fcat_777

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:88826252..88826812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSFCAG00000025490
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_fcat_777
CTATCACAGTTTCAGTTACTTAAAGTTTGCACTTGCCCGACAACACTATTTTCATTCCTAAAGAGATTAACATGCGGATC
TGGCAGTAGACGGAAGTTAAGTGGAGACCAAATAACTTTGCCAACTGCAGTTGATTATTTGTCGGTTCCTAAACAGACAG
ATGCTGAGGAGTGGACGTCCTGGGATGAAGATACACCCACAAGTGTAGATTGAAGGAGGGAATGGGGATGTGATGACACA
ACAAAATACTGTGGAACTGGAACCTGACTATTTTCAGGACATGACACCAACTATAAGGAAAACGTAGAATCATTATTAAG
AAGAGAGAACCATTACATTTTGGCCTCCCAGATGGTAGCACAGGTTTCTCTAGTAGATTAACAGCTACACAATATGTGCC
TTTTATTCGTCAGTCTCCTGAATTAGGCAACTTGGATACCTGGCAGGAAAATACCAACGCATGGGAAGGAGAAGAAGATG
CAGCCTGGCAAGCGGAAGAAGTTCTGAGGCAGCACAAGATGGCAGACAGAGAAAATAAAGGAAGAAAATGGAAAAGGAGG

Alignment

ORF - retro_fcat_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.4 %
• Parental protein coverage: 88.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ITQFRLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQITLPTTVDYSSVPKQADVEEWTSWDEDAPTSV-
          ..QF.L.KVCTC..T.FSFLKRL.C.SG..RKLSGDQITLPT.VDY.SVPKQ.D.EEWTSWDED.PTSV.
Retrocopy LSQFQLLKVCTCPTTLFSFLKRLTCGSGSRRKLSGDQITLPTAVDYLSVPKQTDAEEWTSWDEDTPTSV<

Parental  KIEGGNG-NVTTQQNALEQLEPDYFKDMTPTIRKT-QKIIIKKREPLNFGIPDGSTGFSSRLAATQDMPF
          ....G.G..V.TQQN..E.LEPDYF.DMTPTIRKT...II.K.REPL.FG.PDGSTGFSSRL.ATQ..PF
Retrocopy RLKEGMG<DVMTQQNTVE-LEPDYFQDMTPTIRKT>RIIIKK-REPLHFGLPDGSTGFSSRLTATQYVPF

Parental  LHQSPELGDLDTWQENTNAWEEEEDAAWQAEEVLRQQKIADREKRAAEQQRK
          ..QSPELG.LDTWQENTNAWE.EEDAAWQAEEVLRQ.K.ADRE.......R.
Retrocopy IRQSPELGNLDTWQENTNAWEGEEDAAWQAEEVLRQHKMADRENKGRKWKRR

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	0.11 RPM	28.23 RPM
SRP017611_kidney	0.10 RPM	39.26 RPM
SRP017611_liver	0.00 RPM	15.16 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_777 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_777 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777 ,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,