RetrogeneDB ID: retro_fcat_1838

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:22373463..22373791(-)
• Located in intron of: ENSFCAG00000026385

Retrocopy information

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

Parental gene information

• Parental gene symbol: JTB
• Ensembl ID: ENSFCAG00000012590
• Aliases: None
• Description: jumping translocation breakpoint [Source:HGNC Symbol;Acc:6201]

Sequence

>retro_fcat_1838
GGGAGCCCCCTCTGCTGGCGGTTCTGCGCTCTCACCTCAACGCTCAGCAAGCAGTGGCCCCTGTGCGGGCAGAGATGGCA
GGGAGCACCTCAGGCTTGCCCTGCCGGCTGGTGGAGGACCCTGCGGTGTCAGGAGAATGTGCTCCGTGTGTGAATTCCAG
ACTAAAACCACCTGAGTGTGCTTCCACAGGGTATGTGGAGAAAAATCACATGCAGCTCATCTAAGAGGAATGTTCAAAAG
CTGCCGCTCAGCTCCAGTAGAACAATACTTATTCCAGAAATTCGAAGGGGCCGTCGGAGACGTGCCCTTGGCGTTCGCTG
TGTTCATC

Alignment

ORF - retro_fcat_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSHLCWLLCAFTLKLC-QAEAPVRAEKLSVSTSNLPCWLVEEFVVAEECAPCSNFQAKTTPECGSTGYVE
          GS.LCW..CA.T..L..QA.APVRAE....STS.LPC.LVE...V..ECAPC.N...K..PEC.STGYVE
Retrocopy GSPLCWRFCALTSTLS<QAVAPVRAE-MAGSTSGLPCRLVEDPAVSGECAPCVNSRLKP-PECASTGYVE

Parental  K-ITCSSSKRNEL-KSCRSALMEQHLFWKFEGAVVGVALVFACLV
          K.ITC.SS......KSCRSA..EQ.LF.KFEGAV..V.L.FA...
Retrocopy K>ITC-SSSKRNV>KSCRSAPVEQYLFQKFEGAVGDVPLAFAVFI

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	37.76 RPM
SRP017611_kidney	0.00 RPM	38.13 RPM
SRP017611_liver	0.00 RPM	24.77 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1838 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1838 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002520	1 retrocopy	retro_chof_1297,
Callithrix jacchus	ENSCJAG00000009973	1 retrocopy	retro_cjac_496,
Dasypus novemcinctus	ENSDNOG00000000740	1 retrocopy	retro_dnov_1095,
Echinops telfairi	ENSETEG00000008256	1 retrocopy	retro_etel_1340,
Felis catus	ENSFCAG00000012590	2 retrocopies	retro_fcat_1025, retro_fcat_1838 ,
Myotis lucifugus	ENSMLUG00000013299	1 retrocopy	retro_mluc_2225,
Oryctolagus cuniculus	ENSOCUG00000011788	1 retrocopy	retro_ocun_470,
Procavia capensis	ENSPCAG00000003210	1 retrocopy	retro_pcap_301,
Pongo abelii	ENSPPYG00000000791	1 retrocopy	retro_pabe_1886,
Sus scrofa	ENSSSCG00000006559	1 retrocopy	retro_sscr_687,
Tupaia belangeri	ENSTBEG00000012646	1 retrocopy	retro_tbel_762,