RetrogeneDB ID: retro_fcat_1613

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:22380102..22380916(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BETA-ACTIN
• Ensembl ID: ENSFCAG00000006788
• Aliases: None
• Description: Beta-actin [Source:UniProtKB/TrEMBL;Acc:Q9GLY0]

Sequence

>retro_fcat_1613
CCCAAGAAGCACCCAAGGCTGCTGACTGAGGCCCCCCTGAATGTCAACGCCAACTGAGAGATGATTCAGATCACATTTAG
ACCTGCTGCACTCTGCCTATGTACATGAACATCAGGTCGTGTTGTCCCTGTATACCTCTGGCTATACCACTGGTATTGTT
ATGGAGTCTGGGGGCCAGGTCACTCACACAGTACCCATCTATGAGGGCTGTGCCCTGCCCCATAGCATCCTGTACCTGGT
CCTGGCTGGCTGAGACCTGAAAGACTATCTCACGAAGATCCTCATGTAGCATGCCTGCAGCTTCACCAGACTGGCTGAGT
AAGAAATCCTGAATGACATCATGGAGGTCTGCTATGTCTTGGAGCAGGAGATGGGGTCACTGCTGCATCCTCCTCTTCTC
TGGAGAAGAGTTATGAGCTGCCCAATAGTCAGGTGATCACCATTGGCCACAAGCAGTTCTGGTATCCAGAGGTGCTCTTT
TAGCCCTTTTTCCTGGCTATGGAATCCTGTGGCATCCATGGGACCACCTTCAACTTCCACTGTGAAGTATGATGAGGACA
CACTGTACTCATACAAGGTGCTGTCTGGTGGGACCACCATGTATCCTGGATCACTGACAGGATATGGAAGGACATCATGG
CCCTGGCCCCACAGCACAATGTAGATCAAAAGCATCACTCCTCCTGAACATAGTTAAGTACCCAGCGTGGATGGGGGTTC
CATCCTAGCCTCAGTGTCCACCCTCCAGTGGATGTGGATCAATAAGCAGAAATATGAGGAGGTAGACCCTGCCATTGTTC
TCCACAAATGCTTC

Alignment

ORF - retro_fcat_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 77.22 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PEEHPVLLTEAPLNPKANREKMTQIMFE-TFNTPAMYVAI-QAVLSLYASGRTTGIVMDSGDGVTHTVPI
          P..HP.LLTEAPLN..AN.E.M.QI.F..T..T..MY..I.Q.VLSLY.SG.TTGIVM.SG..VTHTVPI
Retrocopy PKKHPRLLTEAPLNVNAN*E-MIQITFR<TCCTLPMYMNI<QVVLSLYTSGYTTGIVMESGGQVTHTVPI

Parental  YEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMAT-AASS-
          YEG.ALPH.IL.L.LAG.DL.DYL.KIL.....SFT..AE.EI..DI.E..CYV....EQEM....A.S.
Retrocopy YEGCALPHSILYLVLAG*DLKDYLTKILM*HACSFTRLAE*EILNDIME-VCYV---LEQEMGS<TAASS

Parental  SSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN-SIMKCDVDIRKDLYANTVLSGG
          SSLEKSYELP..QVITIG...F..PE.LF.P.FL.MESCGIH.TTFN.S..K.D.D....LY...VLSGG
Retrocopy SSLEKSYELPNSQVITIGHKQFWYPEVLF*PFFLAMESCGIHGTTFN>STVKYDED---TLYSYKVLSGG

Parental  TTMYPG-IADRMQKEITALAP-STMKIKIIAPPERKYSVWIGG-SILASLSTFQQMWISKQEYDESGPSI
          TTMYPG.I.DR..K.I.ALAP.STM.IK.I.PPE........G.SILAS.ST.Q.MWI.KQ.Y.E..P.I
Retrocopy TTMYPG<ITDRIWKDIMALAP>STM*IKSITPPEHS*VPSVDGGSILASVSTLQWMWINKQKYEEVDPAI

Parental  VHRKCF
          V..KCF
Retrocopy VLHKCF

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	366.35 RPM
SRP017611_kidney	0.00 RPM	312.16 RPM
SRP017611_liver	0.00 RPM	167.81 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1613 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1613 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 14 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613 ,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,