RetrogeneDB ID: retro_fcat_700

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:44777473..44778292(+)
• Located in intron of: ENSFCAG00000009726

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSFCAG00000013303
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_fcat_700
GTACACATAGCTGCTAAATTCATCACTCATGCACCCCCAGGGGAATTTAATGCAGTGTTCAAGGATGTCCGGCTACTACT
TAATAATGACAATCTCCTCAGGGAAGGGGCAGCACATGCATTTGCCCAGTATAACATGGGTCAGTTCACGTCTGTGAAGA
TAGAAGGATATGGAGATCAGGTCTTAAGTACAGAACCCGGTGACCTGGGCAATAGCAGATTTTTAGATCCAAAAAACAAA
ATTTCCTTTAAGTTGGATCATGGACGGAAAGAAGCAAGTGACCCCCAGCCAGAGGACGTAGATGGAGGTCTGAAGTCTGG
GAGAGAATCCTGTGACAGTGCTTTAAGGGCCTATGTGAAAGATCGTTATTCCAATGGCTTCCATACTGTTTACGCTAAAA
CTATAGGTGAGCAACAGATCATTACTGCATGTGTTGAAAGCCACCAGTTTTAGCCTAAAACCTTCTGGAATGGTCATTGG
AGATCAGAGTGGAAGTTCACCATCATACGACCTACAGCCCAGGTTGTTGGAGTACTTAAGATTCAGGTTCACTGTTACGA
AGGTGGCAATGTTCAGTTGGTTAGTCATAAAGATGTACAAGATTCAGTAACTGTTTCGAATGAAGTCCAAACTGCCAAGG
AGTTTATTAAAATCATAGAGCATGCGGAAAATGAACATCAGACAGCAATTAGTGAAAACTATCGAACAACGTCACACACC
TCATTCAAGGCCTTGCACCGGCAGCTTCCGGTTACCCGCATGGAAATCGACTGGAACAAGATACTCAGCTACAGGACTGG
CAAAGAAATGCAGAATGCT

Alignment

ORF - retro_fcat_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.5 %
• Parental protein coverage: 95.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLG
          V.IAAKFITHAPPGEFN.VF.DVRLLLNNDNLLREGAAHAFAQYNM.QFT.VKIEGY.DQVL.TE.GDLG
Retrocopy VHIAAKFITHAPPGEFNAVFKDVRLLLNNDNLLREGAAHAFAQYNMGQFTSVKIEGYGDQVLSTEPGDLG

Parental  NSRFLDPRNKISFKFDHLRKEASDPQPEDVDGGLKSWRESCDSALRAYVKDHYSNGFCTDVYAKTIDGQQ
          NSRFLDP.NKISFK.DH.RKEASDPQPEDVDGGLKS.RESCDSALRAYVKD.YSNGF.T.VYAKTI..QQ
Retrocopy NSRFLDPKNKISFKLDHGRKEASDPQPEDVDGGLKSGRESCDSALRAYVKDRYSNGFHT-VYAKTIGEQQ

Parental  TIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEV
          .I.AC.ESHQF.PK.FWNG.WRSEWKFTI..PTAQVVGVLKIQVH.YE.GNVQLVSHKDVQDSVTVSNEV
Retrocopy IITACVESHQF*PKTFWNGHWRSEWKFTIIRPTAQVVGVLKIQVHCYEGGNVQLVSHKDVQDSVTVSNEV

Parental  QTAKEFIKIIEHAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
          QTAKEFIKIIEHAENE.QTAISENY.T.S.T.FKAL.RQLPVTR..IDWNKILSY..GKEMQNA
Retrocopy QTAKEFIKIIEHAENEHQTAISENYRTTSHTSFKALHRQLPVTRMEIDWNKILSYRTGKEMQNA

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	0.23 RPM	22.50 RPM
SRP017611_kidney	0.00 RPM	18.86 RPM
SRP017611_liver	0.00 RPM	26.89 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_700 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_700 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 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700 , retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,