RetrogeneDB ID: retro_mmus_865

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:56667199..56667699(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tada1
• Ensembl ID: ENSMUSG00000026563
• Aliases: Tada1, 2900026B15Rik, D1Ertd251e, Staf42, Tada1l
• Description: transcriptional adaptor 1 [Source:MGI Symbol;Acc:MGI:1196415]

Sequence

>retro_mmus_865
CTTTCGTCTGTTCAATAGAAATTTGATCGTAGATTACTGCCTCCTAGCCCTCTCTGGAGCGTGTTGCTTGTGGTGAAGGA
ACCCCAAAGTGGTGATGGTTTGAAGCTTCATTCTTGTGCAATGAAACTTTCCACTCAGGGTTCACGTGAAGGGAGAATGA
TGGTGCATGAACACTGGCCAGACAATATTGCAGAGGAGGCTGCTTCTGCTGTCATTTATGCTGGGCAGAATCACCTCAAA
GATAACCTGACTCCAGCTGAGTCAAGAAGCAAAGCTTATTGGTTCGGAGATGGCTATTTTAATTGCACCTTTGATAAAAG
TATGGCCCACAGCCTTTCATGAATAGGGTAGTAACTTATAACAATTTAGTCAAAAGTCCTCCAGTGTTTTCTGTTTGCCA
AGACAGTCAGATAAAATCCAGCTCCCCACCTCAACCTGATAAGGCTGAGCAGCAGTCTCCACTCCTGCTGGTGCAGTCTG
GACACATTTTGCTTGTTTCA

Alignment

ORF - retro_mmus_865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.16 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSSVRQKFDHRFQPQNPLSGAQQFVAKEPQGDDDLKLCSHTMMLPTRGQLEGRMIVTAYEHGLDNVTEEA
          LSSV..KFD.R..P..PL......V.KEPQ..D.LKL.S..M.L.T.G..EGRM.V...EH..DN..EEA
Retrocopy LSSVQ*KFDRRLLPPSPLWSVL-LVVKEPQSGDGLKLHSCAMKLSTQGSREGRMMV--HEHWPDNIAEEA

Parental  VSAVVYAVENHLKDILTSVVSRRKAYRVRDGHFKYAFGSNVT-PQPYLKNSVVAYNNLVEGPPAFSAPCA
          .SAV.YA..NHLKD.LT...SR.KAY...DG.F...F......PQP...N.VV.YNNLV..PP.FS....
Retrocopy ASAVIYAGQNHLKDNLTPAESRSKAYWFGDGYFNCTFDKSMA<PQPFM-NRVVTYNNLVKSPPVFSVCQD

Parental  NQ-SPASQPHPDDAEQQAAFLLACSGDTLPAS
          .Q....S.P.PD.AEQQ...LL..SG..L..S
Retrocopy SQIKSSSPPQPDKAEQQSPLLLVQSGHILLVS

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	37.05 RPM
SRP007412_cerebellum	0.00 RPM	35.82 RPM
SRP007412_heart	0.00 RPM	10.55 RPM
SRP007412_kidney	0.00 RPM	16.42 RPM
SRP007412_liver	0.00 RPM	12.94 RPM
SRP007412_testis	0.00 RPM	26.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_865 was not detected

EST

No EST(s) were mapped for retro_mmus_865 retrocopy.

TSS

No TSS is located nearby retro_mmus_865 retrocopy 5' end.

Lab

retro_mmus_865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865 ,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,