RetrogeneDB ID: retro_fcat_1005

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:137036870..137037376(+)
• Located in intron of: ENSFCAG00000014285

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000015224
• Aliases: None
• Description: None

Sequence

>retro_fcat_1005
AAGAAACAGAATGGAAAGAGTAAAAAGTAGAAGAGGCAGAGCCTGAAGAATTTATTGTGGAAAGAGTACAGGAGCAACAT
GTAGTGAATGGGAAGGTGGAGTATTTCCTGAGGTGGAAGGGGTTCACAGATGTTGACGATACTTGGGAACCTGAAGAAAA
TTTAGACTCTCCAGAGTTAATTGAAGCAGTTCTTAGTTCTCAAAAGGCTGGTAAAGAAAAAGATGGCACAAAAAGAAAAT
CTGTATCTGACGGTGGATGTGATGGTAGCAACTCGGAGAAGAAAAGAGATGCTGTGAATAGACCAAGAGGCTTTGCCAGG
AGTTCTTGATCCTGAACGAGGAATTGGTGCCACAGACAGCAGTGGAGAATTCATGTTTCTTGTGAAATGGAAAGATAGGC
AGACTCGGTGCTGGCAAAACAGGCAAATGTGAAATGTTCTCACATTGTGATTGCTTTTTATGAAGAGAGAGTAACCCAGA
ATTCTTGTCCAGAAGCTGAAGCTCAG

Alignment

ORF - retro_fcat_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 93.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKQNGKSKK-VEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK
          KKQNGKSKK.VEEAEPEEF.VE.V....VVNGKVEYFL.WKGFTD.D.TWEPEENLD.PELIEA.L.SQK
Retrocopy KKQNGKSKK<VEEAEPEEFIVERVQEQHVVNGKVEYFLRWKGFTDVDDTWEPEENLDSPELIEAVLSSQK

Parental  AGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARG-LDPERIIGATDSSGELMFLMKWKDSDE-AD
          AGKEKDGTKRKS.SD...D.S.S.KKRDA...PRGFAR..LDPER.IGATDSSGE..F....K..D..AD
Retrocopy AGKEKDGTKRKSVSDGGCDGSNSEKKRDAVNRPRGFARS>LDPERGIGATDSSGE--FMFLVKWKDR<AD

Parental  LVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          .VLAK.AN.KC..IVIAFYEER.T..SCPE.EAQ
Retrocopy SVLAKQANVKCSHIVIAFYEERVTQNSCPEAEAQ

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	31.33 RPM
SRP017611_kidney	0.00 RPM	25.87 RPM
SRP017611_liver	0.00 RPM	21.63 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1005 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1005 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 12 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013843	22 retrocopies	retro_chof_1128, retro_chof_1147, retro_chof_1156, retro_chof_1178, retro_chof_1210, retro_chof_1223, retro_chof_132, retro_chof_1569, retro_chof_1672, retro_chof_1779, retro_chof_1863, retro_chof_1962, retro_chof_222, retro_chof_2269, retro_chof_2347, retro_chof_2379, retro_chof_2435, retro_chof_2695, retro_chof_411, retro_chof_676, retro_chof_87, retro_chof_936,
Cavia porcellus	ENSCPOG00000015168	1 retrocopy	retro_cpor_66,
Dasypus novemcinctus	ENSDNOG00000006250	19 retrocopies	retro_dnov_1136, retro_dnov_1174, retro_dnov_1208, retro_dnov_1270, retro_dnov_1605, retro_dnov_2306, retro_dnov_2307, retro_dnov_2397, retro_dnov_2543, retro_dnov_2605, retro_dnov_2633, retro_dnov_321, retro_dnov_359, retro_dnov_385, retro_dnov_445, retro_dnov_772, retro_dnov_794, retro_dnov_833, retro_dnov_844,
Felis catus	ENSFCAG00000006056	1 retrocopy	retro_fcat_514,
Felis catus	ENSFCAG00000015224	6 retrocopies	retro_fcat_1005 , retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Homo sapiens	ENSG00000122565	9 retrocopies	retro_hsap_1071, retro_hsap_1145, retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Microcebus murinus	ENSMICG00000006998	11 retrocopies	retro_mmur_1015, retro_mmur_1030, retro_mmur_1076, retro_mmur_1178, retro_mmur_1497, retro_mmur_1500, retro_mmur_1548, retro_mmur_386, retro_mmur_421, retro_mmur_68, retro_mmur_685,
Nomascus leucogenys	ENSNLEG00000014931	9 retrocopies	retro_nleu_141, retro_nleu_1685, retro_nleu_2462, retro_nleu_373, retro_nleu_397, retro_nleu_511, retro_nleu_676, retro_nleu_944, retro_nleu_964,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Sorex araneus	ENSSARG00000008011	2 retrocopies	retro_sara_496, retro_sara_709,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,