RetrogeneDB ID: retro_fcat_152

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:44200243..44200652(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S1
• Ensembl ID: ENSFCAG00000029169
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 1 subunit [Source:HGNC Symbol;Acc:559]

Sequence

>retro_fcat_152
TTAATGGGATTCTTGAAACTGTTCGGCGGGCTGGAGGAGTTGCGGCTGCTACAGTGGTACATGGCCTTGTCAGACAAACA
ACGAAATAAGGTGGCTTGAGAACTTACACGGTCGTTCTGGCTTGCAAGCTCATGGTGTGCGGCTTCCTGGAGAGAACGGA
CCTTAAAATCGTCTATAAAAGATATGCCAGCCTCTACCTCTGCTGCGCCTTTGAGCGCCGGGACAATGAGCTCCTTATGC
TGGAGCTGACTCACCGAGGTGGTGAGCTCCTGGACGAATACTTGCCCAGCATGTGCGAGATGGACATCATCTTTAACTGT
GAGAAAGTCTGTTTCATCTAGTATGAGGTTTTGATACGGGAGATGCCCAGGACAGCTTCAAGAAGAGCGTGCTGAAGTCT
GTGACTCAG

Alignment

ORF - retro_fcat_152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 86.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMRFMLLFSRQGKLRLQKWYLATSDKERKKMVRELMQ-VVLARKPKMCSFLEWRDLKVVYKRYASLYFCC
          .M.F..LF.....LRL..WY.A.SDK.R.K...EL...VVLA.K...C.FLE..DLK.VYKRYASLY.CC
Retrocopy LMGFLKLFGGLEELRLLQWYMALSDKQRNKVA*ELTR<VVLACKLMVCGFLERTDLKIVYKRYASLYLCC

Parental  AIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLM-GGDVQDTSKKSVLKAIEQ
          A.E..DNEL..LEL.HR..ELLD.Y..S.CE.DIIFN.EK..FI..E.L...GD.QD..KKSVLK...Q
Retrocopy AFERRDNELLMLELTHRGGELLDEYLPSMCEMDIIFNCEKVCFI*YEVLI<TGDAQDSFKKSVLKSVTQ

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	0.23 RPM	66.91 RPM
SRP017611_kidney	0.00 RPM	35.66 RPM
SRP017611_liver	0.00 RPM	13.95 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_152 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_152 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002673	1 retrocopy	retro_amel_210,
Felis catus	ENSFCAG00000029169	1 retrocopy	retro_fcat_152 ,
Homo sapiens	ENSG00000106367	1 retrocopy	retro_hsap_3765,
Macropus eugenii	ENSMEUG00000016245	3 retrocopies	retro_meug_1011, retro_meug_154, retro_meug_2051,
Microcebus murinus	ENSMICG00000005406	2 retrocopies	retro_mmur_1026, retro_mmur_1368,
Myotis lucifugus	ENSMLUG00000009898	2 retrocopies	retro_mluc_1493, retro_mluc_2061,
Mustela putorius furo	ENSMPUG00000015867	1 retrocopy	retro_mputfur_1184,
Pan troglodytes	ENSPTRG00000019520	3 retrocopies	retro_ptro_1234, retro_ptro_24, retro_ptro_2554,