RetrogeneDB ID: retro_mmus_1914

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:49308154..49309459(+)
• Located in intron of: ENSMUSG00000036792

Retrocopy information

• Ensembl ID: ENSMUSG00000081272
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ap2m1
• Ensembl ID: ENSMUSG00000022841
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:MGI Symbol;Acc:MGI:1298405]

Sequence

>retro_mmus_1914
ATGATCGGAGGCTTATTCATCTATAATCACAAGGGGGAGGTGCTTATCTCCCGGGTCTACAGAGATGACATCGGGAGGAA
TGCTGTGGATGCCTTTCGGGTCAATGTCATTCATGCACGGCAGCAGGTGCGCAGCCCTGTCACAAACATCGCTCGCACCA
GCTTCTTCCATGTTAAGCGGTCCAACATCTGGCTGGCCGCAGTCACCAAGCAGAATGTCAATGCTGCCATGGTCTTCGAA
TTCCTCTACAAGATGTGTGATGTAATGGCTGCTTACTTTGGCAAAATCAGCGAGGAGAACATCAAGAACAATTTTGTGCT
CATATACGAGCTGCTGGATGAGATTCTGGACTTTGGCTACCCACGGAACTCAGAGATAGGTGCACTGAAAACCTTCATCA
CCCAGCAGGGTATCAAGAGTCAGCATCAGACGAAGGAAGAACAGTCCCAGATCACCAGCCAGGTGACCGGGCAGATTGGC
TGGCGGCAAGAAGGCATCAAGTATCGCCGGAATGAACTCTTCCTAGATGTTCTGGAGAGTGTGAACCTGCTTATGTCCCC
ACAGGGGCAGGTGCTGAGTGCCCATGTGTCAGGCCGGGTGGTGATGAAGAGTTACCTGAGTGGCATGCCTGAGTGCAAGT
TTGGAATGAATGACAAGATTGTCATAGAAAAGCAGGGCAAAGGCACAGCTGATGAAACAAGCAAGAGTGGTAAGCAGTCG
ATCGCCATTGATGACTGCACCTTCCACCAGTGTGTGCGACTCAGCAAGTTTGACTCTGAGCGGAGCATCAGCTTCATCCC
TCCCGATGGAGAGTTTGAACTCATGAGATACCGTACTACCAAGGACATCATCCTTCCTTTCCGGGTGATCCCATTGGTGC
GGGAGGTGGGGCGCACCAAACTGGAGGTCAAGGTGGTCATCAAGTCCAACTTCAAGCCCTCACTTCTGGCCCAGAAGATT
GAGGTGAGGATCCCGACTCCATTGAACACAAGCGGGGTACAGGTGATCTGCATGAAGGGGAAGGCCAAGTACAAGGCCAG
CGAGAACGCCATTGTATGGAAGATCAAGCGCATGGCAGGCATGAAGGAATCCCAGATCAGCGCAGAGATTGAGCTCCTGC
CCACCAACGATAAGAAGAAATGGGCTCGGCCCCCCATTTCCATGAACTTTGAGGTGCCATTCGCGCCTTCTGGCCTCAAG
GTGCGCTACTTGAAGGTATTCGAACCGAAGCTGAACTACAGCGACCATGATGTCATCAAATGGGTGCGATACATTGGCCG
CAGTGGCATTTATGAAACCCGCTGC

Alignment

ORF - retro_mmus_1914 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK
          MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK
Retrocopy MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK

Parental  QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS
          QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYP.NSE.GALKTFITQQGIKS
Retrocopy QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPRNSEIGALKTFITQQGIKS

Parental  QHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP
          QHQTKEEQSQITSQVTGQIGWR.EGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP
Retrocopy QHQTKEEQSQITSQVTGQIGWRQEGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP

Parental  ECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTT
          ECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTT
Retrocopy ECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTT

Parental  KDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA
          KDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA
Retrocopy KDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA

Parental  IVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
          IVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
Retrocopy IVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK

Parental  WVRYIGRSGIYETRC
          WVRYIGRSGIYETRC
Retrocopy WVRYIGRSGIYETRC

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
SRP007412_brain	13.99 RPM	173.07 RPM
SRP007412_cerebellum	9.60 RPM	120.06 RPM
SRP007412_heart	2.15 RPM	60.17 RPM
SRP007412_kidney	5.49 RPM	93.71 RPM
SRP007412_liver	3.55 RPM	71.93 RPM
SRP007412_testis	1.14 RPM	27.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1914 was not detected

EST

No EST(s) were mapped for retro_mmus_1914 retrocopy.

TSS

No TSS is located nearby retro_mmus_1914 retrocopy 5' end.

Lab

retro_mmus_1914 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1914 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 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	ENSMUSG00000021824	1 retrocopy	retro_mmus_580,
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,