RetrogeneDB ID: retro_fcat_692

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:34168493..34169030(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSFCAG00000027765
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_fcat_692
TATTATACCATCAGTGGTCATAATGCAAAAGTAAGAAAGGTTTTGTGTAGACAAGAAATGCAGGAAGGCCAAAGTTCTAG
AAGTGGAAGAGGAGGAAACTTTGGTTTTGGAGATTCTCCTGGTGGTGGTAGAAATTTTGGACAAGGACCAAGAAATAATT
TTAGGGGAGGATCTGATGCATATGAAGTGGTTGTGGATTTGGGGATGGTTGTAATGGGTATGGAAGAGAACTAACAGGTG
GCAATTTTAGAGGTAGCCCTGGTTATGGATGAGGAAGAAGAAGATATGGTGGTGGGGGACCTGGATGTAGCAACCAGGAT
GGGGGCTATAGAGGTGGTTATGACAACTGTGGAGGAGGAAATTATGGAAGTGGAAATTACAATGGTTTTGGAAATTATAC
CTACTAACCTTGTAACTATGGTCCAATGAAAGTGGAATCTTTGGGGGTACCAGGAACATGTGAGGCCATATGGTGGAGGC
AACTATGGTCCTAGAGGCAACTATGGTCCTACAGGCAGTGGAGGAAGTGGGGGTTAT

Alignment

ORF - retro_fcat_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.85 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGGGNFGPGPGSNFRGGSDGYG-SGRGFGD
          Y.TI.GHNA.VRK.L.RQEMQE.QSSRSGRGGNFGFGDS.GGG.NFG.GP..NFRGGSD.Y..SG.GFGD
Retrocopy YYTISGHNAKVRKVLCRQEMQEGQSSRSGRGGNFGFGDSPGGGRNFGQGPRNNFRGGSDAYE<SGCGFGD

Parental  GYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYGGGYDNYGGGNYGSGNYNDFGNYNQQPSN
          G.NGYG....GGNF.GSPGYG.GR..YGGGGPG..NQ.GGY.GGYDN.GGGNYGSGNYN.FGNY...P.N
Retrocopy GCNGYGRELTGGNFRGSPGYG*GRRRYGGGGPGCSNQDGGYRGGYDNCGGGNYGSGNYNGFGNYTY*PCN

Parental  YGPMK-SGNFGGSRNMGG-PYGGGNYGPGGSGGSGGYGGRSRY
          YGPMK.SG.FGG.RNM.G.PYG...............GG...Y
Retrocopy YGPMK<SGIFGGTRNM*G<PYGXXXXXXXXXXXXXXXGGSGGY

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	529.22 RPM
SRP017611_kidney	0.21 RPM	784.17 RPM
SRP017611_liver	0.00 RPM	458.44 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_692 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_692 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 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis	ENSCING00000004062	1 retrocopy	retro_cint_7,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
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 ,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Mus musculus	ENSMUSG00000004980	1 retrocopy	retro_mmus_573,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,