RetrogeneDB ID: retro_cfam_1254

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:44131257..44132241(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000031581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAPK3
• Ensembl ID: ENSCAFG00000017108
• Aliases: None
• Description: mitogen-activated protein kinase 3 [Source:HGNC Symbol;Acc:6877]

Sequence

>retro_cfam_1254
ATCGGCGAGGGCGCGTACGGCATGGTCAGCTCAGCTGACGACCACGTGCGCAAGGTTCGCGTGGCCATCAAGAAAATCAG
CCCCTTTGAGCATCAGACCTACTGCCAGCGCACACTGAGGGAGATCCAGATCTTGCTGCGCTTCCGCCATGAGAACGTCA
TTGGCATTCGGGACATTCTGCGGGCGCCCACCCTGGACGCCATGAGGGATGTCTACATCGTGCAGGACCTGATGGAGACA
GACCTATACAAGTTGCTCAAAAGCCAGCAGCTGAGCAACGACCATGTTTGCTACTTCCTCTACCAGATCCTGCGAGGCCT
CAAGTATATCCACTCAGCCAATGTGCTCCACCGGGATTTAAAGCCCTCTAACCTGCTCATCAACACCACCTGCGACCTTA
AGATCTGCGATTTTGGCCTGGCCCGGATTGCCGATCCTGAGCATGACCACACTGGCTTCCTGACAGAATATGTGGCCACG
CGCTGGTACCGGGCTCCAGAAATCATGCTTAACTCTAAGGGCTACACCAAGTCCATCGACATCTGGTCTGTGGGCTGCAT
TCTGGCTGAGATGCTCTCCAACCGGCCCATCTTCCCTGGCAAGCACTACCTGGACCAGCTCAACCACATTCTAGGTATCC
TAGGTTCTCCATCCCAGGAGGACTTGAACTGTATCATCAATATGAAGGCCCGAAACTACCTACAGTCTCTGCCCTCCAAG
ACCAAGGTGGCATGGGCCAAGCTTTTTCCCAAGTCAGACTCCAAAGCCCTTGACCTGCTAGACCGGATGTTGACCTTTAA
CCCCAACAAACGGATTACAGTGGAAGAAGCACTGGCTCATCCCTACTTGGAGCAGTACTACGACCCAACAGATGAGCCAG
TGGCTGAGGAGCCTTTCACTTTCGACATGGAGCTGGATGATCTACCCAAGGAGCGTCTGAAGGAGCTCATCTTCCAGGAG
ACAGCCCGCTTCCAGCCTGGGGTG

Alignment

ORF - retro_cfam_1254 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.56 %
• Parental protein coverage: 90.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGKGCLGFSHSAYDHVRKVRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRAPTLDAMRD
          .G.G..G...SA.DHVRKVRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRAPTLDAMRD
Retrocopy IGEGAYGMVSSADDHVRKVRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRAPTLDAMRD

Parental  VYIVQDLMETDLYKLLKSQQLSNDHVCYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGL
          VYIVQDLMETDLYKLLKSQQLSNDHVCYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGL
Retrocopy VYIVQDLMETDLYKLLKSQQLSNDHVCYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGL

Parental  ARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
          ARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
Retrocopy ARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI

Parental  LGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAH
          LGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAH
Retrocopy LGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAH

Parental  PYLEQYYDPTDEPVAEEPFTFDMELDDLPKERLKELIFQETARFQPGV
          PYLEQYYDPTDEPVAEEPFTFDMELDDLPKERLKELIFQETARFQPGV
Retrocopy PYLEQYYDPTDEPVAEEPFTFDMELDDLPKERLKELIFQETARFQPGV

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
SRP012049_cerebellum	26.80 RPM	17.72 RPM
SRP017611_brain	30.72 RPM	28.82 RPM
SRP017611_kidney	9.38 RPM	9.05 RPM
SRP017611_liver	3.55 RPM	2.83 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1254 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017108	1 retrocopy	retro_cfam_1254 ,
Dasypus novemcinctus	ENSDNOG00000002191	1 retrocopy	retro_dnov_1241,
Loxodonta africana	ENSLAFG00000017904	1 retrocopy	retro_lafr_1022,
Myotis lucifugus	ENSMLUG00000011284	1 retrocopy	retro_mluc_1697,
Mus musculus	ENSMUSG00000063065	1 retrocopy	retro_mmus_2694,
Pongo abelii	ENSPPYG00000007239	1 retrocopy	retro_pabe_1440,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831,