RetrogeneDB ID: retro_mmus_1873

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:38703643..38704324(-)
• Located in intron of: ENSMUSG00000024998

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1873
ATGATTGGAGGCTTATTCATCTATAATCATAAGGGGGAGGTGCTTATCTCCCGGGTCTACAGAGATGACATCGGGAGGAA
TGCTGTGGATGCCTTTCGGGTCAATGTCATTCATGCACGGCAGCAGGCGCGCAGCCCTGTCACAAACATCGCTTGCACCA
GCTTCTTCTATGTTAAGTGGTCCAACATCTGGCTGGCCGCAGTCACCAAGCAGAATGTCAATGCTGCCATGGTCATTGAA
TTCCTCTACAAGATGTGTGATATAATGGCTGCTTACTTTGGCAAGATCAGCGAGGAGAACATCAAGAACAATTTTGTGCT
CGTATACGAGCTGCTGGATGAGATTCTGGACTTTGGCTACCCACAGAACTCAGAGACAGGTGCACTGAAGACCTTCATCA
CCCAGCAGGGTATCGAGAGTCAGCATCAGATGAAGGAAGAACAGTCCCAGATCACCAGCCAGGTGACCGGGCAGATTGGC
TGGCGGCGAGAAGGCATCAAGTATCGCCGGAATGAACTCTTCCTAGATGTTCTGGAGAGTGTGGGCCTGCTTATGTCCCC
ACAGGGGCAGGTGCTGAGTGCCCGTGTGTCAGGCCGAGTGGTGATGAAGAGTTACCTGAGTGGCATGCCTGAGTGCAAGT
TTGGAATGAATGACAAGATTGTCATAGAAAAGCAGGGCAGG

Alignment

ORF - retro_mmus_1873 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 52.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK
          MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQ.RSPVTNIA.TSFF.VK.SNIWLAAVTK
Retrocopy MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQARSPVTNIACTSFFYVKWSNIWLAAVTK

Parental  QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS
          QNVNAAMV.EFLYKMCD.MAAYFGKISEENIKNNFVL.YELLDEILDFGYPQNSETGALKTFITQQGI.S
Retrocopy QNVNAAMVIEFLYKMCDIMAAYFGKISEENIKNNFVLVYELLDEILDFGYPQNSETGALKTFITQQGIES

Parental  QHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP
          QHQ.KEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESV.LLMSPQGQVLSA.VSGRVVMKSYLSGMP
Retrocopy QHQMKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVGLLMSPQGQVLSARVSGRVVMKSYLSGMP

Parental  ECKFGMNDKIVIEKQGK
          ECKFGMNDKIVIEKQG.
Retrocopy ECKFGMNDKIVIEKQGR

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	0.07 RPM	173.07 RPM
SRP007412_cerebellum	0.04 RPM	120.06 RPM
SRP007412_heart	0.12 RPM	60.17 RPM
SRP007412_kidney	0.13 RPM	93.71 RPM
SRP007412_liver	0.03 RPM	71.93 RPM
SRP007412_testis	0.00 RPM	27.03 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1873 was not detected

EST

No EST(s) were mapped for retro_mmus_1873 retrocopy.

TSS

No TSS is located nearby retro_mmus_1873 retrocopy 5' end.

Lab

retro_mmus_1873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1873 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,