RetrogeneDB ID: retro_fcat_1561

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D3:70384366..70384925(-)
• Located in intron of: ENSFCAG00000012954

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSFCAG00000012904
• Aliases: None
• Description: ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]

Sequence

>retro_fcat_1561
AGCTGCAAAGCCTCCCATAACACCCTGTACGAGGCGGTGCGGGAAGTCCTGCACGGGAACCAGCGTGGGTGCCGGAAGTT
TTGGGAGATGGTGGAGCTGCATATCACCTTGAATATCTGTGGCTCTCAGAAGGACAAATCCTTCTTGGGCACCATTGGGC
TTAAGTCCACTCCCTGCCTGAAGTTCTCTGTATGTGTTTTGGGGGACCAGCAACGCTTGATGAGGCCAAGGCTGTGGATA
TTCCCCACATGGACATTGATGTGCTGAAGAACTCAACAGGAATAAAAAACTAGGCAAGAAGCTGGCCAAGAAGTGTGATG
CCTTTTTGGCTTCATAATCTTTGATCGAGTAGATCCTGTGAATCCTGGGCCCGGGACTTAATAAGGCTGGCAAGTTCCCT
TCCTTGTTGACCCGCAGTGAGAACATGGTGGCCAGAATGGATGAAGTGAAGTCCACGATCAAATTCCAGATGAAGAAGGT
GCTGTGTCTGGCATGAACGTTACAGATGATAAGCTTGCATACAACAGCTGTCAGTTTCCTGGTGTCATTGCTCAAGAAC

Alignment

ORF - retro_fcat_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.25 %
• Parental protein coverage: 86.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ
          S.K.S..TLYEAVREVLHGNQR..RKF.E.VEL.I.L.....QKDK.F.GT..LKSTP..KFSVCVLGDQ
Retrocopy SCKASHNTLYEAVREVLHGNQRGCRKFWEMVELHITLNICGSQKDKSFLGTIGLKSTPCLKFSVCVLGDQ

Parental  QHC-DEAKAVDIPHMDIEALK-KLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLT
          Q...DEAKAVDIPHMDI..LK..LN.NKKL.KKLAKK.DAFLAS.SLI..I..ILGPGLNKAGKFPSLLT
Retrocopy QRL<DEAKAVDIPHMDIDVLK<ELNRNKKLGKKLAKKCDAFLAS*SLIE*IL*ILGPGLNKAGKFPSLLT

Parental  HNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVN
          ..ENMVA..DEVKSTIKFQMKKVLCLA..................L..N
Retrocopy RSENMVARMDEVKSTIKFQMKKVLCLA*TLQMISLHTTAVSFLVSLLKN

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	101.46 RPM
SRP017611_kidney	0.00 RPM	356.48 RPM
SRP017611_liver	0.00 RPM	174.28 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1561 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1561 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 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000670	13 retrocopies	retro_amel_1144, retro_amel_1223, retro_amel_1262, retro_amel_1591, retro_amel_1813, retro_amel_198, retro_amel_318, retro_amel_320, retro_amel_417, retro_amel_520, retro_amel_609, retro_amel_710, retro_amel_970,
Echinops telfairi	ENSETEG00000013325	2 retrocopies	retro_etel_1974, retro_etel_326,
Felis catus	ENSFCAG00000012904	7 retrocopies	retro_fcat_1144, retro_fcat_1488, retro_fcat_1561 , retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens	ENSG00000198755	13 retrocopies	retro_hsap_142, retro_hsap_1462, retro_hsap_1710, retro_hsap_177, retro_hsap_1935, retro_hsap_2795, retro_hsap_3025, retro_hsap_3245, retro_hsap_3353, retro_hsap_337, retro_hsap_3949, retro_hsap_4025, retro_hsap_4040,
Gorilla gorilla	ENSGGOG00000028140	10 retrocopies	retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Macaca mulatta	ENSMMUG00000015907	6 retrocopies	retro_mmul_1931, retro_mmul_2041, retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Nomascus leucogenys	ENSNLEG00000008650	13 retrocopies	retro_nleu_1174, retro_nleu_1210, retro_nleu_1697, retro_nleu_1778, retro_nleu_1980, retro_nleu_2055, retro_nleu_2342, retro_nleu_2436, retro_nleu_2879, retro_nleu_662, retro_nleu_838, retro_nleu_986, retro_nleu_989,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Oryctolagus cuniculus	ENSOCUG00000004065	2 retrocopies	retro_ocun_130, retro_ocun_4,
Rattus norvegicus	ENSRNOG00000000505	4 retrocopies	retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Tursiops truncatus	ENSTTRG00000009431	6 retrocopies	retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,