RetrogeneDB ID: retro_cfam_1923

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:44980..46284(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010650
• 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_1923
CTGATTGGAGGCTTATTCATCTATAATCACAAGGGGGAGGTGCTCCTCTCCCAGGTCTACCGAGATGACACCGGGAGGAA
TGCAGTGGATGCTTTCGGGTCAATGTTATCCACACCCGGCAGCAGGTGTGCAGCCCCATCACCAACATCGCTCGCACCAG
TTTCTTCCATGTTAAGCGGTCCAACATCTGGTTGGCAGCTGTCACCAAGCAGAATGTCAATGCTGCCATGGTCTTTGAAT
TCCTCTATAAGATGTGTGACGTAATGGCTGCCTACTTTGGCAAGATCAGCGAGGAGAATATCAAGAACAATTTTGGGCTC
ATATATGAGCTGCTGGATGAGATCCTGGACTTTGGCTATCCACAGAATTCAGAGACAGGAGCACTGAAAATCTTCATCAC
TCAGCAGGGTATCAAGAGCCAGCATCAGACAAAAGAAGAGCAATCCCAGATCACCAGCCAGGTGACTGGGCAGATTGGTT
GGCAGTGGGAGGGCATCAAGTATCGCCGGAATGAGCTCTTCTTGGATGTGCTGGAAAGTGTGAACCTCCTCATGTCCCCA
CAGGGGCAGGTGCTAAGTGCCCATGTGTCAGACCGGGTGGTGATAAAGAGCTACCTGAGTGGCATGCCTGAATGCAAGTT
TGGGATGAATGACAAGATTGTCATTGAGAAGCAAGGCAAAGGCACAGCTGATGAAACAAGCAAGAACGGAAAGCAATCAA
TTGCCATCGATGACTGCACCTTCCACCAGTGTGTGCGACTCAGAAAGTTTGACTCTGAACGCAGCATCAGCTTCATCCCA
CCAGATGGAGAGTTTGAGCTAATGAGGTATCGCACCACCAAGGACATCATCCTTCCTTTCCGGGTGATCCCAGTAGTGCG
AGAACTGGGACGCACCAAGCTGGAGGTCAAGGTGGTCATCAAATCCAATTTCAAACCCTCTTTACTGGCTCAGAAGATTG
AGGTGAGGATCCCAACTCTACTGAATACAAGCGGGGTACAGGTGATGTGCATGAAGGGGAAGGCCAAGTGCAAGGCCAGA
GAGAACGCCATCGTGTGGAAGATAAAGCGCGTGGCAGGCTTGAAGGAATCGCAGATCAACGCAGAGATTGAACTTCTGCC
CGCCAATGACAAGAAGAAATGGGCTCGACCCCCCATTTCCATGAACTTTGAGGTGCCATTCGCACCCTCTGGCCTCAAGG
TGCGCTACTTGAAGGTGTTTGAACCGAAGCTGAACTACAGCGACCATGATGTCATCAAATGGGTGCACTACATTGGCCAC
GGTGGCATTTATGAGACCCGCTGC

Alignment

ORF - retro_cfam_1923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.89 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAF-RVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVT
          .IGGLFIYNHKGEVL.S.VYRDD.GRNAVDAF.RVNVIH.RQQV.SP.TNIARTSFFHVKRSNIWLAAVT
Retrocopy LIGGLFIYNHKGEVLLSQVYRDDTGRNAVDAF<RVNVIHTRQQVCSPITNIARTSFFHVKRSNIWLAAVT

Parental  KQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIK
          KQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNF.LIYELLDEILDFGYPQNSETGALK.FITQQGIK
Retrocopy KQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFGLIYELLDEILDFGYPQNSETGALKIFITQQGIK

Parental  SQ--TKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGM
          SQ..TKEEQSQITSQVTGQIGW..EGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVS.RVV.KSYLSGM
Retrocopy SQHQTKEEQSQITSQVTGQIGWQWEGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSDRVVIKSYLSGM

Parental  PECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRT
          PECKFGMNDKIVIEKQGKGTADETSK.GKQSIAIDDCTFHQCVRL.KFDSERSISFIPPDGEFELMRYRT
Retrocopy PECKFGMNDKIVIEKQGKGTADETSKNGKQSIAIDDCTFHQCVRLRKFDSERSISFIPPDGEFELMRYRT

Parental  TKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
          TKDIILPFRVIP.VRE.GRTKLEVKVVIKSNFKPSLLAQKIEVRIPT.LNTSGVQV.CMKGKAK.KA.EN
Retrocopy TKDIILPFRVIPVVRELGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTLLNTSGVQVMCMKGKAKCKAREN

Parental  AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVI
          AIVWKIKR.AG.KESQI.AEIELLP.NDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVI
Retrocopy AIVWKIKRVAGLKESQINAEIELLPANDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVI

Parental  KWVRYIGRSGIYETRC
          KWV.YIG..GIYETRC
Retrocopy KWVHYIGHGGIYETRC

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	7.77 RPM	390.29 RPM
SRP017611_brain	12.31 RPM	421.18 RPM
SRP017611_kidney	6.34 RPM	258.60 RPM
SRP017611_liver	1.45 RPM	82.59 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1923 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1923 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,