RetrogeneDB ID: retro_mmus_1689

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:9495620..9496340(+)
• Located in intron of: None

Retrocopy information

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

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_1689
ATGGCGGCGCTGTATGCCTGCACCAAGTGCCACCAGCGCTTCCCCTTCGAGGTGCTGTCTCAGGGGCAGAAGCTGTGCAA
GGAATGCCGGATTGCTCACCCTGTTGTGAAGTGTACCTACTGCAGGACCGAGTACCAGCAGGAGAGTAAAACCAATACAA
TTTGCAAGAAGTGTGCTCAGAATGTACAGGTATATGAAACGCCTAAGCCTTGTCAGTATTGCAACATAATTGCTGCATTT
ATTGGGAATAAATGCCAGCGCTGCTCGAATTCAGAGAAGTATGGATCCCCATATTCCTGTGAACAGTGTAAGCAGCAGTG
TGCATTTGACAGAAAGGATGATCGAAAGAAGGTGGGATGCTGGCTGTGCACGCTGTTGTACAAGCGTGTCCTTCAGAAGA
CCAAAGAGCAGAGGAAGCACCTGAGCAGCTCTTCTCAAGGCAGCCATCAGGAGAAGGAGCAGTACAGCCGCCTGAGTGGA
GGCAGCCATTACAACAGCCAGAAAACACTTTCTACATCTTCAATTCAAAATGAAATCCCAAAGAAAAAAATCCAAGTTTG
AGTCAATCACAACTAACAGAGACAGCTTTTCTCCAGACCTGGCTCTGGATTTCCCAGGCACTGACCCTTTGTCATCATTG
CTCAGCTGAAGGAAGAGGTGGCCACTCTGAAGAAGATGTTGCATCAGAAGGATCAAGTGATCCTAGAGAAAGAGCTGAAG

Alignment

ORF - retro_mmus_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.5 %
• Parental protein coverage: 79.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAALYACTKCHQRFPFEALSQGQQLCKECRIAHPVVKCTYCRTEYQQESKTNTICKKCAQNVQLYGTPKP
          MAALYACTKCHQRFPFE.LSQGQ.LCKECRIAHPVVKCTYCRTEYQQESKTNTICKKCAQNVQ.Y.TPKP
Retrocopy MAALYACTKCHQRFPFEVLSQGQKLCKECRIAHPVVKCTYCRTEYQQESKTNTICKKCAQNVQVYETPKP

Parental  CQYCNIIAAFIGNKCQRCTNSEKKYGPPYSCEQCKQQCAFDRKDDRKKVDGKLLCWLCTLSYKRVLQKTK
          CQYCNIIAAFIGNKCQRC.NSE.KYG.PYSCEQCKQQCAFDRKDDRKKV.....CWLCTL.YKRVLQKTK
Retrocopy CQYCNIIAAFIGNKCQRCSNSE-KYGSPYSCEQCKQQCAFDRKDDRKKVG----CWLCTLLYKRVLQKTK

Parental  EQRKHLSSSSRGSHQEKEQYSRLSGGSHYNSQKTLSTSSIQNEIPK-KKSKFESITTNGDSFSPDLALDS
          EQRKHLSSSS.GSHQEKEQYSRLSGGSHYNSQKTLSTSSIQNEIPK.KKSKFESITTN.DSFSPDLALD.
Retrocopy EQRKHLSSSSQGSHQEKEQYSRLSGGSHYNSQKTLSTSSIQNEIPK>KKSKFESITTNRDSFSPDLALDF

Parental  PGTD-HFVIIAQLKEEVATLKKMLHQKDQMILEKEKK
          PGTD..FVIIAQLKEEVATLKKMLHQKDQ.ILEKE.K
Retrocopy PGTD<PFVIIAQLKEEVATLKKMLHQKDQVILEKELK

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	0.02 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	0.05 RPM	17.78 RPM
SRP007412_testis	0.09 RPM	150.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1689 was not detected

EST

No EST(s) were mapped for retro_mmus_1689 retrocopy.

TSS

No TSS is located nearby retro_mmus_1689 retrocopy 5' end.

Lab

retro_mmus_1689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1689 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,