RetrogeneDB ID: retro_cfam_1650

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:23595201..23595783(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000014550
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AMN1
• Ensembl ID: ENSCAFG00000010668
• Aliases: None
• Description: antagonist of mitotic exit network 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:27281]

Sequence

>retro_cfam_1650
TGCCTGTGGTGCTTCATGAAGAATATTTCCAGATATATCACAGACATTAAGCCTTTGCCTCCCAACATAAAAGATAGACT
GATTAAAATAATGAGTACCCAGGGGCAGATAACAGATTCAAATATAAGTGTGATTTTACATCCTGAAGTCCAAACACTAG
ATCTAAGAAGCTGTGACATTTCAGATACTGCTCTCCTACACCTGTGCAACTGCAGAAAATTAAAGAAATTAAATATAAGT
TCCTCAAAAGAAAACAGAATTTCCATAACTTCAAAAGGAATAAAAGCTGTGGCTTCCTCTTGTTCATACGTCCATGAAGC
TTCTTTGAAAAGATGTTGCAATCTTACTGACGAAGGAGTCCTTGCTCTTGCACTCAACTGCCGGCTGTTAAAGATCATTG
ATTTAGGTGGCTGTTTAGGAATTACTGATGTGTCCTTACATGCATTGGGAGAAAACTGCCCATTTTTGCAGTGTGTTGAT
TTTTCAGCTACTCAGGTATCTGATGATGGTGTAGTTGCTCTTGTTAATGGACCTTGTGCCAAGAAATTAGAGGAGATTCA
TATGGGACTTTGTGTAAATCTG

Alignment

ORF - retro_cfam_1650 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.45 %
• Parental protein coverage: 74.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLWCFMKNISRYITDIKPLPPNIKDRLIKIMSTQGQITDSNISEILHPEVQTLDLRSCDISDTALLHLCN
          CLWCFMKNISRYITDIKPLPPNIKDRLIKIMSTQGQITDSNIS.ILHPEVQTLDLRSCDISDTALLHLCN
Retrocopy CLWCFMKNISRYITDIKPLPPNIKDRLIKIMSTQGQITDSNISVILHPEVQTLDLRSCDISDTALLHLCN

Parental  CRKLKKLNISSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNCRLLKIIDLGGCLG
          CRKLKKLNISSSKENRISITSKGIKAVASSCSY.HEASLKRCCNLTDEGVLALALNCRLLKIIDLGGCLG
Retrocopy CRKLKKLNISSSKENRISITSKGIKAVASSCSYVHEASLKRCCNLTDEGVLALALNCRLLKIIDLGGCLG

Parental  ITDVSLHALGENCPFLQCVDFSATQVSDDGVVALVNGPCAKKLEEIHMGHCVNL
          ITDVSLHALGENCPFLQCVDFSATQVSDDGVVALVNGPCAKKLEEIHMG.CVNL
Retrocopy ITDVSLHALGENCPFLQCVDFSATQVSDDGVVALVNGPCAKKLEEIHMGLCVNL

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	2.73 RPM	10.04 RPM
SRP017611_brain	1.67 RPM	16.12 RPM
SRP017611_kidney	1.12 RPM	6.80 RPM
SRP017611_liver	0.36 RPM	4.13 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1650 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1650 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014156	1 retrocopy	retro_btau_1488,
Canis familiaris	ENSCAFG00000010668	1 retrocopy	retro_cfam_1650 ,
Choloepus hoffmanni	ENSCHOG00000008485	2 retrocopies	retro_chof_1418, retro_chof_1459,