RetrogeneDB ID: retro_fcat_1066

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:117244350..117244782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIA
• Ensembl ID: ENSFCAG00000009159
• Aliases: PPIA, MT-ND1, MTND1, NADH1, ND1, cypA
• Description: Peptidyl-prolyl cis-trans isomerase A [Source:UniProtKB/Swiss-Prot;Acc:Q8HXS3]

Sequence

>retro_fcat_1066
ATCTCCAAGCTGTTTGCAGACAAAGTTCCAAAAATGGCAGAGAACTTCCATGCTCTAAGCATTGGGGAGAAAGGACTTGG
TTATAAAGGTTCCTGCTTTCACAGGATTATTCTGGGATTTATGTGCCAGGGTGGTGACTTCACATGCCATGATGGCACTG
GCAGCAGGTCCATCTATGGGGAGAAATTTGATGATGAGAGTTTCATCCTGAAGCACACAGGTCCTGGCATCTTGTCCACG
GCAAATGCTGGACCCAACACAAACGGTTCCGAGTTTTTCACGTGCACTGCTAAGACTGAGTGGTTGGATGGCAAGCACGT
GGTGTCTGGCAAGTTGAAGGAGGGCATGAACACTGTGGAAGCCATGAGGCATTTTGGGTCCAGGAATGGCAAGACCAGCA
AGAAGATCACCACTGCTGACTGTGGACAAATC

Alignment

ORF - retro_fcat_1066 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.03 %
• Parental protein coverage: 93.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLQLFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFDDENFIL
          ...LFADKVPK.AENF.ALS.GEKG.GYKGSCFHRII.GFMCQGGDFT.H.GTG..SIYGEKFDDE.FIL
Retrocopy ISKLFADKVPKMAENFHALSIGEKGLGYKGSCFHRIILGFMCQGGDFTCHDGTGSRSIYGEKFDDESFIL

Parental  KHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGMVKEGMNIVEAMERFGSRNGKTSKKITIAD
          KHTGPGILS.ANAGPNTNGS.FF.CTAKTEWLDGKHVV.G..KEGMN.VEAM..FGSRNGKTSKKIT.AD
Retrocopy KHTGPGILSTANAGPNTNGSEFFTCTAKTEWLDGKHVVSGKLKEGMNTVEAMRHFGSRNGKTSKKITTAD

Parental  CGQI
          CGQI
Retrocopy CGQI

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	0.69 RPM	129.35 RPM
SRP017611_kidney	1.24 RPM	193.34 RPM
SRP017611_liver	1.52 RPM	71.07 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1066 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1066 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 8 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017784	30 retrocopies	retro_amel_1032, retro_amel_1036, retro_amel_1141, retro_amel_1259, retro_amel_1264, retro_amel_1440, retro_amel_1516, retro_amel_1520, retro_amel_1524, retro_amel_1687, retro_amel_1713, retro_amel_1731, retro_amel_1786, retro_amel_1862, retro_amel_266, retro_amel_365, retro_amel_398, retro_amel_528, retro_amel_537, retro_amel_555, retro_amel_621, retro_amel_656, retro_amel_692, retro_amel_707, retro_amel_721, retro_amel_76, retro_amel_763, retro_amel_793, retro_amel_812, retro_amel_984,
Choloepus hoffmanni	ENSCHOG00000011597	12 retrocopies	retro_chof_1071, retro_chof_1276, retro_chof_1317, retro_chof_1335, retro_chof_1876, retro_chof_1955, retro_chof_1959, retro_chof_2687, retro_chof_336, retro_chof_632, retro_chof_652, retro_chof_929,
Felis catus	ENSFCAG00000009159	18 retrocopies	retro_fcat_1066 , retro_fcat_1146, retro_fcat_12, retro_fcat_1324, retro_fcat_133, retro_fcat_1348, retro_fcat_1517, retro_fcat_1710, retro_fcat_1733, retro_fcat_1739, retro_fcat_1914, retro_fcat_1928, retro_fcat_372, retro_fcat_504, retro_fcat_531, retro_fcat_676, retro_fcat_684, retro_fcat_827,
Macropus eugenii	ENSMEUG00000002016	20 retrocopies	retro_meug_1024, retro_meug_1055, retro_meug_1089, retro_meug_1133, retro_meug_1269, retro_meug_1391, retro_meug_1576, retro_meug_1746, retro_meug_1880, retro_meug_1975, retro_meug_2013, retro_meug_2037, retro_meug_260, retro_meug_297, retro_meug_301, retro_meug_437, retro_meug_478, retro_meug_510, retro_meug_713, retro_meug_73,
Monodelphis domestica	ENSMODG00000016089	9 retrocopies	retro_mdom_1373, retro_mdom_1524, retro_mdom_1856, retro_mdom_1884, retro_mdom_215, retro_mdom_272, retro_mdom_29, retro_mdom_730, retro_mdom_85,
Mustela putorius furo	ENSMPUG00000018190	2 retrocopies	retro_mputfur_101, retro_mputfur_22,
Sorex araneus	ENSSARG00000007250	1 retrocopy	retro_sara_484,
Sarcophilus harrisii	ENSSHAG00000017062	3 retrocopies	retro_shar_164, retro_shar_383, retro_shar_750,