RetrogeneDB ID: retro_cfam_2028

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373298.1:21593..22904(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000024548
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSCAFG00000012257
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:HGNC Symbol;Acc:564]

Sequence

>retro_cfam_2028
GCTGCTGCCATGATTGGAGGCTTATTCATCTATAATCACAAGGGGGAGGTGCTCCTCTCCCAGGTCTACCGAGATGACAC
CGGGAGGAATGCAGTGGATGCCTTTCGGGTCAATGTTATCCACGCCTGGCAGCAGGTGTGCAGCCCCATCACCAACATCG
CTCGCACCAGTTTCTTCCATGTTAACCGGTCCAACATCTGGTTGGCAGCTGTCACCAAGCAGAATGTCAATGCTGCCATG
GTCTTCGAATTCCTCTATAAGATGTATGATGTAATGGCTGCCTACTTTGGCAAGATCAGTGAGGAGAACATCAAGAACAA
TTTTGGGCTCATATATGAGCTGCTGGATGAGAATCTGGACTTTGGCTATCCACAGAATTCAGAGACAGGAGCACTGAAAA
TCTTCATCACTCAGCAGGGTATCAAGAGCCAGCATCAGACAAAAGAGCAATCCCAGATCACCAGCCAGGTGACTGGGCAG
ATTGGCTGGCAGCGGGAGGGCATCAAGTATCGCCGGAATGAGCTCTTCTTGGATGTGCTGGAAAGTGTGAACCTCCTCAT
GTCCCCACAGGGGCAGGTGCTAAGTGCCCATGTGTCAGGCCGGGTGGTGATGAAGAGCTACCTGAGTGGCATGCCTGAAT
GCAAGTTTGGGATGAATGACAAGATTGTCATTGAGAAACAAGGCAAAGTCACAGCTGATGAAACAAGCAAGAGCGGAAAG
CAATCAATTGCCATCGATGACTGCACCTTCCACCAGTGTGTGCGACTCAGCAAGTTTGACTCTGAACGCAGCATCAGCTT
CATCCCACCAGATGGAGAGTTTGAGCTAATAAGGTATTGCACCCCCAAGGACATCATCCTTCCTTTCCGGGTGATCCCAC
TAGTGCGAGAACTGGGACACACCAAGCTGGAGGTCAAGGTGGTCATCAAATCCAATTTCAAACCTTCTTTACTGGTTCAG
AAGATTGAGGTGAGGATCCCAACTCTACTGAATACAAGCGGGGTACAGGTGATCTGCATGAAGGGGAAGGCCAAGTGCAA
GGCCAGCGAGAACGCCATCGTGTAGAAGATAAAGCGCATGGCAGGCTTGAAGGAATCGCAGATCAACGCAGAGATTGAAC
TTCTGCCCGCCAATGACAAGAAGAAATGGGCTCGACCCCCCATTTCCATGAACTTTGAGGTGCCATTCGCACTCTCTGGC
CTCAAGGTGCGCTACTTGAAGGTGTTTGAACCGAAGCTGAACTACAGCTACCATGATGTCATCAAATGGGTGCACTACAT
TGGCCACAGCGGCATTTATGAGACCCGCTGC

Alignment

ORF - retro_cfam_2028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAMIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAA
          AAAMIGGLFIYNHKGEVL.S.VYRDD.GRNAVDAFRVNVIHA.QQV.SP.TNIARTSFFHV.RSNIWLAA
Retrocopy AAAMIGGLFIYNHKGEVLLSQVYRDDTGRNAVDAFRVNVIHAWQQVCSPITNIARTSFFHVNRSNIWLAA

Parental  VTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQG
          VTKQNVNAAMVFEFLYKM.DVMAAYFGKISEENIKNNF.LIYELLDE.LDFGYPQNSETGALK.FITQQG
Retrocopy VTKQNVNAAMVFEFLYKMYDVMAAYFGKISEENIKNNFGLIYELLDENLDFGYPQNSETGALKIFITQQG

Parental  IKSQTK-EEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSG
          IKSQ....EQSQITSQVTGQIGW.REGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSG
Retrocopy IKSQHQTKEQSQITSQVTGQIGWQREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSG

Parental  MPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYR
          MPECKFGMNDKIVIEKQGK.TADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFEL.RY.
Retrocopy MPECKFGMNDKIVIEKQGKVTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELIRYC

Parental  TTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASE
          T.KDIILPFRVIPLVRE.G.TKLEVKVVIKSNFKPSLL.QKIEVRIPT.LNTSGVQVICMKGKAK.KASE
Retrocopy TPKDIILPFRVIPLVRELGHTKLEVKVVIKSNFKPSLLVQKIEVRIPTLLNTSGVQVICMKGKAKCKASE

Parental  NAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDV
          NAIV.KIKRMAG.KESQI.AEIELLP.NDKKKWARPPISMNFEVPFA.SGLKVRYLKVFEPKLNYS.HDV
Retrocopy NAIV*KIKRMAGLKESQINAEIELLPANDKKKWARPPISMNFEVPFALSGLKVRYLKVFEPKLNYSYHDV

Parental  IKWVRYIGRSGIYETRC
          IKWV.YIG.SGIYETRC
Retrocopy IKWVHYIGHSGIYETRC

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	3.19 RPM	390.29 RPM
SRP017611_brain	4.29 RPM	421.18 RPM
SRP017611_kidney	2.18 RPM	258.60 RPM
SRP017611_liver	0.80 RPM	82.59 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2028 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2028 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020106	1 retrocopy	retro_btau_1156,
Canis familiaris	ENSCAFG00000012257	2 retrocopies	retro_cfam_1923, retro_cfam_2028 ,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Otolemur garnettii	ENSOGAG00000012286	1 retrocopy	retro_ogar_1110,
Rattus norvegicus	ENSRNOG00000001709	1 retrocopy	retro_rnor_2342,
Tursiops truncatus	ENSTTRG00000008493	1 retrocopy	retro_ttru_522,