RetrogeneDB ID: retro_mmus_2783

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:119892919..119893454(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080719
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam76a
• Ensembl ID: ENSMUSG00000028878
• Aliases: None
• Description: family with sequence similarity 76, member A [Source:MGI Symbol;Acc:MGI:2385211]

Sequence

>retro_mmus_2783
TGCACCAAATGCCACCAGCACTTCCCCTTTGAGGTGATGTCTCAGGGGCGGAAGCTGTGCAAGGAATGCCAGATTGCCCA
CCTTGTTGTGAAGTGCACCTACTGCGGGACTGAGCACCAGCAGGAGAGTAAAACCAATACAATGTGCAAGAAGTGTGCTC
AGAATGTACCGTTATATGGAACACCTAACCCTTGTCAGTATTGCAACATAACTGCTACATTTATTGGGAATAAAGGCCAG
CGCTGCACAAATTCAGAGAGGAAGTATGGACCCCCATACTCCTGTGAACAGTGCAAGCAGCAGTGTGCATTTGACAGGAA
GGATGATAGAAAGAAGGTGGGTGGGAGGCTGCTATGCTGGCTGTGCACAGTCATACAAGTGTGTCCTTCAGAAGACCAAA
GAGCAGAGGAAGCACCTGAGCAGCTCTTCTCGCAGCAGCCATCGGGAGAAGGAGCAGTCCAACTGCCTGAGTGGTGACAG
CCATTACAGCAGCCAGAAAACACTTTCTACATCAATTCAAAATGAAATCCCAAAG

Alignment

ORF - retro_mmus_2783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.9 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CTKCHQRFPFEALSQGQQLCKECRIAHPVVKCTYCRTEYQQESKTNTICKKCAQNVQLYGTPKPCQYCNI
          CTKCHQ.FPFE..SQG..LCKEC.IAH.VVKCTYC.TE.QQESKTNT.CKKCAQNV.LYGTP.PCQYCNI
Retrocopy CTKCHQHFPFEVMSQGRKLCKECQIAHLVVKCTYCGTEHQQESKTNTMCKKCAQNVPLYGTPNPCQYCNI

Parental  IAAFIGNKCQRCTNSEKKYGPPYSCEQCKQQCAFDRKDDRKKVDGKLLCWL-CTLSYKRVLQKTKEQRKH
          .A.FIGNK.QRCTNSE.KYGPPYSCEQCKQQCAFD...D..K..G..L....C..SYK.VLQKTKEQRKH
Retrocopy TATFIGNKGQRCTNSERKYGPPYSCEQCKQQCAFD-RKDDRKKVGGRLLCW>CAQSYKCVLQKTKEQRKH

Parental  LSSSSRGSHQEKEQYSRLSGGSHYNSQKTLSTSSIQNEIPK
          LSSSSR.SH.EKEQ...LSG.SHY.SQKTLST.SIQNEIPK
Retrocopy LSSSSRSSHREKEQSNCLSGDSHYSSQKTLST-SIQNEIPK

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	0.00 RPM	41.54 RPM
SRP007412_cerebellum	0.00 RPM	22.88 RPM
SRP007412_heart	0.00 RPM	29.70 RPM
SRP007412_kidney	0.00 RPM	32.53 RPM
SRP007412_liver	0.00 RPM	17.78 RPM
SRP007412_testis	0.05 RPM	150.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2783 was not detected

EST

No EST(s) were mapped for retro_mmus_2783 retrocopy.

TSS

No TSS is located nearby retro_mmus_2783 retrocopy 5' end.

Lab

retro_mmus_2783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2783 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
Callithrix jacchus	ENSCJAG00000009327	1 retrocopy	retro_cjac_3197,
Mus musculus	ENSMUSG00000028878	2 retrocopies	retro_mmus_1689, retro_mmus_2783 ,
Ochotona princeps	ENSOPRG00000017049	1 retrocopy	retro_opri_911,