RetrogeneDB ID: retro_fcat_1178

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:42889561..42889979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSFCAG00000029786
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_fcat_1178
ATGCTGTCTCTAGATTTTTTGGATGATGTGCAGCGAATGGACAAGCGGCAGCTGTATTATCAAGTCCTAAATTTTGGAAT
GATAGTTTCCTCAGCACTAATGATCTGGAAGGGGTTAATGGTCATAACTGGAAGTCAAAGTCCAATTGTAGTTGCTCAGT
GGCAGCACGGAACCTGCATTTCATAGAGGAGATCTTCTCTTTTTAACAAATGGAGTTGAAGATCCCATCCGAGTGGGAGA
AATTGTTTTTAGGATAGAAGGAAGAGAGATTCCTATAGTTCGTGGAGTCTTGAAGATTCGTGAAAAGCAAAATGGACATA
TCAAGTTTTTGGCCAAAGGAGATAATAATGCGGTTGATGACAGAGGCCTCTATAAACAAGGACAACACTGGCTGGAGAAG
AAGGATGTCGTGGGGAGA

Alignment

ORF - retro_fcat_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.85 %
• Parental protein coverage: 78.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSLDFLDDVRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVV-LSGSMEPAFHRGDLLFL
          MLSLDFLDDV.RM.KRQLYYQVLNFGMIVSSALMIWKGLMVITGS.SP..VV.LSGS.EPAFHRGDLLFL
Retrocopy MLSLDFLDDVQRMDKRQLYYQVLNFGMIVSSALMIWKGLMVITGSQSP-IVV>LSGSTEPAFHRGDLLFL

Parental  TNRVEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVV
          TN.VEDPIRVGEIV.FRIEGREIPIV..VLKI.EKQNGHIKFL.KGDNNAVDDRGLYKQGQHWLEKKDVV
Retrocopy TNGVEDPIRVGEIV-FRIEGREIPIVRGVLKIREKQNGHIKFLAKGDNNAVDDRGLYKQGQHWLEKKDVV

Parental  GR
          GR
Retrocopy GR

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	11.94 RPM
SRP017611_kidney	0.00 RPM	43.80 RPM
SRP017611_liver	0.10 RPM	42.26 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1178 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1178 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178 , retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,