RetrogeneDB ID: retro_fcat_1231

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:175930796..175931395(-)
• Located in intron of: ENSFCAG00000014741

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSFCAG00000012146
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_fcat_1231
GATAAGGTTGATAAAATTGTTGTTCAGAAATACCATACTACTAATGGGCATAATTGTGAAGTGGAAAAGGCTGTTTCTCA
ACAAGAAATGCAGTCTTCTAGATCACAAAGAGGTCATGGAGTTGGATCTGGCAACTTTATGGGTCGTGGAGGAAACTTTA
GAGGTGGCTGTAGCTTTGGCCATGGTGGAAACTTTGGTGGAAGAGAAGGCTATGGTGGTGGAGACAATGGCAGCAGAGGT
AGTTTTGGAGGAGGTGATGGTGGATAAAGTGTATTTGGAGGTGATGGTGGCAACTATGGAGGTAGTCCTGGTTGCAATAG
TAGAGGAGGCTATGGTGGTGGTGGACCAGGATATGGAAACCAAGGAGGCAGATTTGGCTTTGGTGGTGGAGGATATAATG
CTTACCATGAAGGAGGAAATGTTGGAGGCAACTATGGTGGTGGTGGGAACCATATGATTTTGGAAATTATAGAGGACAAT
AGCAATCAAATTATAGACTCATGAAGGGGGCAGTTTTGGTGGAAGAAATGTGGGCTTGTCCCTACAGTAATGGTTATGGA
TCTGGTGGTGGAAGTGGTGGATATGGTGGTACAAGCTTC

Alignment

ORF - retro_fcat_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 53.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGGGGNFGRGGNFGGRGG
          D.VDKIVVQKYHT.NGHNCEV.KA.S.QEMQS..SQRG.G.GSGNFMGRGGNF.GG..FG.GGNFGGR.G
Retrocopy DKVDKIVVQKYHTTNGHNCEVEKAVSQQEMQSSRSQRGHGVGSGNFMGRGGNFRGGCSFGHGGNFGGREG

Parental  YGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGGYGGGGGGYDGYNEGGN
          YGGG..GSRGS.GGGDGG...FGGDGGNYGG.PG..SRGGYGGGGPGYGNQGG..G.GGGGY..Y.EGGN
Retrocopy YGGGDNGSRGSFGGGDGG*SVFGGDGGNYGGSPGCNSRGGYGGGGPGYGNQGGRFGFGGGGYNAYHEGGN

Parental  FGGGNYGGGGNY-NDFGNYSGQQQSNYGPMK-GGSFGGRSSG-SPYGGGYGSGGGSGGYGSRRF
          ..GGNYGGGGN...DFGNY.GQ.QSNY..MK.GGSFGGR..G..PY..GYGSGGGSGGYG...F
Retrocopy V-GGNYGGGGNH<YDFGNYRGQ*QSNYRLMK<GGSFGGRNVG>CPYSNGYGSGGGSGGYGGTSF

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	86.19 RPM
SRP017611_kidney	0.00 RPM	104.71 RPM
SRP017611_liver	0.00 RPM	54.69 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1231 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1231 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 19 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Felis catus	ENSFCAG00000010150	9 retrocopies	retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231 , retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Felis catus	ENSFCAG00000027765	1 retrocopy	retro_fcat_692,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,