RetrogeneDB ID: retro_fcat_1176

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:41544998..41545886(-)
• Located in intron of: ENSFCAG00000025351

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSFCAG00000001936
• Aliases: None
• Description: karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]

Sequence

>retro_fcat_1176
AACAACCAGGGCAGTGTAAGTTGATCTGTTAATAGCATTGTCAAAAGCATAAATAGCAACAATTTGGAAAGCCACCTCCA
GGCTACTCGAGCTGCTAAGAAACTGCTTTCTGGGGAAAAGTAGCCCCCATAGAGAACATCATCTGGCTTGGTTTCATTCC
AAAATTTGTGTCCTTTTTGGACAGAATTGTTTGTAGTCCCATTCAGTTGAATCTGCTTGAGCTCTCACTAACATTGCTTC
TAGAATATCAGAACAGACCAAGGCTGTGGTAGATAGAGGTGCTGTCCCAGCATTCATTTCTCCATTGACATCTTCCCATG
CTCGCATCAGCGAACAAGCTGTATGAGCTCTAGGAAACATTGTACGCGATAGTTCAGTTTTCTGAGATTTGGTCTTCAAG
TATGGTACATTTGACCCACTGTTGGCCCTTCTTGCAGTTTCTGATATGTCGTCTGTAGCATGTGGTTACTTAGGTAATCT
TATCTGGACGCTTCCAAATTTTTGTTACAGAAAGGATCCTGTACTCCTGTAGATGCTGTTAAGCAACTTCTTCCTATTTT
AGTTCTTCTCCTACATTATGGTGATCCAGAAGTATTGGCAGACACCTGCTGGACCATTTCTTACCAGACTGGTGGTCCAA
ATGAGCAGATAAAAGTGGTTGTTGAAAGGGGAGTTGTGCCCCAACTTGTAATGCTTCTAAGAGCTCCTAAATTGTCAATT
GTGACTTCTGTGCTAAGAGCCATAGGAAGTATTGTCACTGGGACAGATGAACCGACTCATGTTATAATAGAAGTGGGAGC
ACTTGCCATCTTCCCCAGCCTGGTAATGAGCCCCAAAACTAATACTCAGAAGGAAGCAGTGTGGACGGTGTGAAACATCA
CAGCTGGT

Alignment

ORF - retro_fcat_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.67 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NNQGTVNWSVDDIVKGINSNNLESQLQATQAARKLLSREKQPP-IDNIIRAGLIPKFVSFLGRTDCSPIQ
          NNQG.V..SV..IVK.INSNNLES.LQAT.AA.KLLS.EK.PP.I.NII..G.IPKFVSFL.R..CSPIQ
Retrocopy NNQGSVS*SVNSIVKSINSNNLESHLQATRAAKKLLSGEK*PP<IENIIWLGFIPKFVSFLDRIVCSPIQ

Parental  F-ESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASSHAHISEQAVWALGNIAGDGSVFRDLVIKYGAV
          ..ESA.ALTNIAS..SEQTKAVVD.GA.PAFIS.L.SSHA.ISEQAV.ALGNI..D.SVF.DLV.KYG..
Retrocopy L<ESA*ALTNIASRISEQTKAVVDRGAVPAFISPLTSSHARISEQAV*ALGNIVRDSSVF*DLVFKYGTF

Parental  DPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPA-PPLDAVEQILPTLVRLLHHDDPEVLADTCWAI
          DPLLALLAV.DMSS.ACGYL.NL.WTL.N.C..K.P...P.DAV.Q.LP.LV.LLH..DPEVLADTCW.I
Retrocopy DPLLALLAVSDMSSVACGYLGNLIWTLPNFCYRKDPV<TPVDAVKQLLPILVLLLHYGDPEVLADTCWTI

Parental  SYLTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLT
          SY.T.GPNE.I..VV..GVVPQLV.LL.A..L.IVT..LRAIG.IVTGTDE.T.V.I..GALA.FPSL..
Retrocopy SYQTGGPNEQIKVVVERGVVPQLVMLLRAPKLSIVTSVLRAIGSIVTGTDEPTHVIIEVGALAIFPSLVM

Parental  NPKTNIQKEATWTMSNITAG
          .PKTN.QKEA.WT..NITAG
Retrocopy SPKTNTQKEAVWTV*NITAG

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	15.04 RPM
SRP017611_kidney	0.31 RPM	11.03 RPM
SRP017611_liver	0.10 RPM	8.59 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1176 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1176 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 23 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176 , retro_fcat_921,
Homo sapiens	ENSG00000182481	1 retrocopy	retro_hsap_2950,
Gorilla gorilla	ENSGGOG00000027535	2 retrocopies	retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus	ENSOCUG00000015913	4 retrocopies	retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Pteropus vampyrus	ENSPVAG00000004976	2 retrocopies	retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,
Tupaia belangeri	ENSTBEG00000006274	14 retrocopies	retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos	ENSVPAG00000001855	3 retrocopies	retro_vpac_124, retro_vpac_162, retro_vpac_163,