RetrogeneDB ID: retro_fcat_1677

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E1:62541215..62541733(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL45
• Ensembl ID: ENSFCAG00000005808
• Aliases: None
• Description: mitochondrial ribosomal protein L45 [Source:HGNC Symbol;Acc:16651]

Sequence

>retro_fcat_1677
CCCCATCCCAGCGGCCTGTGTGGGAACAAAATGGCAGCCCCCATGCTGCGGGGTTTGTCTTGTTTATCCAGAGCTTTAGG
ATGGTGGTCTGGGCAGCCAGTCCTGGTAACTCAGTCCACAGTTGTAGTTCCAGTGAGATCTAAACAACGTTTCACACCAC
CTACTTATGACCCAAATACAAATCAGAAAAGGAGTTTATAGAACATGCCCAGAAAGCAGGACTGGTCATTCCTCTGGAAC
GTTTGGAGCATCCCCTACACCTGGCCTGTACAGCTGGCACCTTTGATGCCTATGTTCCTCTAGAGGGTGATGCTCACTTG
TCCTCTCTCTTGAAGGAAGGACTGGCACAGAGAAGTGAGTGGTTGAAGAAGAAGGTGACATCACAATTGTCAGTCCGGAA
GATAAGAGAACATGATCCGAATTTGAAAATAAAGGACTTCCCTGAAAAAGCTAAGGATATTTTTATTGAAGCCCACTTTT
GTCTAAACAACTCAGACCATGACTGACTTCATACCTTG

Alignment

ORF - retro_fcat_1677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 53.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PHPSGLCGNKMAAPTLRGLCCLSRALGWWSRQPVLVTQSTVVVPVRTKKRFTPPTYEP-KYKSEKEFIEH
          PHPSGLCGNKMAAP.LRGL.CLSRALGWWS.QPVLVTQSTVVVPVR.K.RFTPPTY.P.KYKSEKEFIEH
Retrocopy PHPSGLCGNKMAAPMLRGLSCLSRALGWWSGQPVLVTQSTVVVPVRSKQRFTPPTYDP<KYKSEKEFIEH

Parental  ARKAGLVIPPERLERPLHLACTAGIFDAYVPPEGDARLSSLSKEGLAQRSERLKKKVTSQLSMIKLREHD
          A.KAGLVIP.ERLE.PLHLACTAG.FDAYVP.EGDA.LSSL.KEGLAQRSE.LKKKVTSQLS..K.REHD
Retrocopy AQKAGLVIPLERLEHPLHLACTAGTFDAYVPLEGDAHLSSLLKEGLAQRSEWLKKKVTSQLSVRKIREHD

Parental  PNFKIKDFPEKAKDIFIEAHLCLNNSDHDRLHTL
          PN.KIKDFPEKAKDIFIEAH.CLNNSDHD.LHTL
Retrocopy PNLKIKDFPEKAKDIFIEAHFCLNNSDHD*LHTL

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	11.13 RPM
SRP017611_kidney	0.00 RPM	23.19 RPM
SRP017611_liver	0.00 RPM	14.66 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1677 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1677 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677 , retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512,