RetrogeneDB ID: retro_fcat_1502

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D2:25374722..25375738(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000029692
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000008729
• Aliases: None
• Description: None

Sequence

>retro_fcat_1502
ATGGTGAAAGAAACTACTTACTGTGATGTTTGGGGGTCAAACCCAGTGCTACCCAGGAAGAATTGAAAAAGGCTTACAGG
AAACTGGCTTTGAAGTACCACCCTGACAAGAATCCAAATGAAGGAGAGAAGTTTAAACAGATTTCTCAAGCTTATGAAGT
GCTCTCTGATGCAAAGAAAAGGGAATTATATGACAAAGGAGGAGAACAGGCAATTAAAGAAGGTGGAGGAGGCAGTGGTT
TGGACTCTCCCATGGACACCTTTGATATGTTTTTTGGAGGAGGAGGAAGGATGCAGAGAGAAGGGAGAAGTGAAAATGTT
GTACATCAGCTCTCTGTAACCTTAGGAGATTTATGTAACAGTGCAATAAGAAAACCAGTTCTGTAGAAGAATGTGATTTG
CGACAAATGTGAAGGCCAAGGTGGTAAGAAAGGAGTCGTAGAATGTTGTCCCAATGGCTGAGGTACTAGAGTGCAAATAA
GAATTCATCAGACAGGACCTGGAATGGTTCAGCAAATTCAATCTGTGTGCATTGAGTGCCAGGACCCTAGGGAATGGATC
AGTCCTAAAGATAGATGTAAAAGCTGCAATAGAAGGAAGAGAATTCGAGAAAGGAAGATTCTAGAAGTTCATATTGACAA
GGGCATAAAAGATGGCCAGAAAATAACATTCCATGGTGAAGGAGACTAAGAACCAGGACTGGAGCCACGAGCTATTATCA
TTATTTTAGATCAGAAGGGCCATGCTGTTTTTACTTGGTGAGGAGAGGATCTTCTCTTGTATATGGACATACAGCTGGTT
GGAGCACTGTATGGCTTTCAAAAGCCAATATCTACTCGTGACAACAGAACCATTGTCATCACCTCTCACCCAGGTCAGAC
TGTCAAGCAGGGAGATACCAAGTGTGCTAAACGAAGGCGTGCCAATTTATTGTAGGGTGAATATGAAAAGGGTCACCAAT
TCATCAAAATTAAGGTAAACTTTCCTGAGAGCGGCTTTCTCTCTCCTGATAAACTC

Alignment

ORF - retro_fcat_1502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.71 %
• Parental protein coverage: 85.39 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDV-LGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGE
          MVKETTY.DV.LGVKP.ATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGE
Retrocopy MVKETTYCDV<LGVKPSATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGE

Parental  QAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEG
          QAIKEGG.G.G..SPMD.FDMFFGGGGRMQRE.R..NVVHQLSVTL.DL.N.A.RK..L.KNVICDKCEG
Retrocopy QAIKEGGGGSGLDSPMDTFDMFFGGGGRMQREGRSENVVHQLSVTLGDLCNSAIRKPVL*KNVICDKCEG

Parental  RGGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILE
          .GGKKG.VECCPN..GT..QIRIHQ.GPGMVQQIQSVC.ECQ...E.ISPKDRCKSCN.RK..RE.KILE
Retrocopy QGGKKGVVECCPNG*GTRVQIRIHQTGPGMVQQIQSVCIECQDPREWISPKDRCKSCNRRKRIRERKILE

Parental  VHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPIST
          VHIDKG.KDGQKITFHGEGD.EPGLEP..III.LDQK.HAVFT..GEDL...MDIQLV.AL.GFQKPIST
Retrocopy VHIDKGIKDGQKITFHGEGD*EPGLEPRAIIIILDQKGHAVFTW*GEDLLLYMDIQLVGALYGFQKPIST

Parental  LDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKL
          .DNRTIVITSHPGQ.VK.GD.KC............YEKG...I..KVNFPE.GFLSPDKL
Retrocopy RDNRTIVITSHPGQTVKQGDTKCAKRRRANLL*GEYEKGHQFIKIKVNFPESGFLSPDKL

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	104.44 RPM
SRP017611_kidney	0.10 RPM	45.04 RPM
SRP017611_liver	0.00 RPM	55.80 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1502 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1502 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 18 parental genes, and 114 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus	ENSBTAG00000016265	6 retrocopies	retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Choloepus hoffmanni	ENSCHOG00000000631	9 retrocopies	retro_chof_1760, retro_chof_186, retro_chof_2020, retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
Dasypus novemcinctus	ENSDNOG00000018342	3 retrocopies	retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502 , retro_fcat_1984, retro_fcat_811,
Homo sapiens	ENSG00000086061	4 retrocopies	retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Pongo abelii	ENSPPYG00000019141	4 retrocopies	retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes	ENSPTRG00000020852	4 retrocopies	retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Sus scrofa	ENSSSCG00000011000	2 retrocopies	retro_sscr_134, retro_sscr_984,
Tupaia belangeri	ENSTBEG00000000596	23 retrocopies	retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tursiops truncatus	ENSTTRG00000007387	4 retrocopies	retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,