RetrogeneDB ID: retro_mmus_1626

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:21968489..21968775(-)
• Located in intron of: ENSMUSG00000053347

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mycbp
• Ensembl ID: ENSMUSG00000028647
• Aliases: Mycbp, 5730488M09Rik, AW552132, AW742590, Amy-1
• Description: c-myc binding protein [Source:MGI Symbol;Acc:MGI:1891750]

Sequence

>retro_mmus_1626
TCAGACTGGAAGCACAAGTAGTTATAGAGGTACTAGTGGAGGTCCAGGGTGCTGGACACTGTGGCATAAGTGTTGGTAGC
CTTAAATGAAGAACCACAGAACCGGGCCAGTGCTCTGGAATTTTTAAAGTATCATTTAGGAGCTGCTACCATGAAAAACC
CAGAAATAGAGCTGCTTTGCCTAGAACTGGCAGAAATGATAGAGAAAGCTACTGTAGACAAAAAGAAACAAACTGAAAGC
AAAACTTGCTCAAAGTGAGCCACCTCAGGAGGAGAAGCATGCTGAA

Alignment

ORF - retro_mmus_1626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.31 %
• Parental protein coverage: 94.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADSKREQFRRYLEKSGVLDTLTKVLVALYEEPEKPTSALDFLKHHLGAATPENPEIELLRLELAEMKEKY
          .D.K.....RY...S.VLDT...VLVAL.EEP....SAL.FLK.HLGAAT..NPEIELL.LELAEM.EK.
Retrocopy SDWKHK*L*RY*WRSRVLDTVA*VLVALNEEPQNRASALEFLKYHLGAATMKNPEIELLCLELAEMIEK-

Parental  EATVEENK-KLKAKLVQYEPPQEEKRAE
          .ATV...K.KLKAKL.Q.EPPQEEK.AE
Retrocopy -ATVDKKK>KLKAKLAQSEPPQEEKHAE

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	4.60 RPM
SRP007412_cerebellum	0.00 RPM	7.73 RPM
SRP007412_heart	0.00 RPM	7.50 RPM
SRP007412_kidney	0.02 RPM	13.94 RPM
SRP007412_liver	0.00 RPM	10.30 RPM
SRP007412_testis	0.00 RPM	19.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1626 was not detected

EST

No EST(s) were mapped for retro_mmus_1626 retrocopy.

TSS

No TSS is located nearby retro_mmus_1626 retrocopy 5' end.

Lab

retro_mmus_1626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1626 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030622	1 retrocopy	retro_cfam_1618,
Choloepus hoffmanni	ENSCHOG00000013136	3 retrocopies	retro_chof_1349, retro_chof_151, retro_chof_610,
Callithrix jacchus	ENSCJAG00000036558	1 retrocopy	retro_cjac_5,
Cavia porcellus	ENSCPOG00000020447	1 retrocopy	retro_cpor_1195,
Homo sapiens	ENSG00000214114	2 retrocopies	retro_hsap_1649, retro_hsap_2251,
Gorilla gorilla	ENSGGOG00000005810	2 retrocopies	retro_ggor_1245, retro_ggor_1678,
Loxodonta africana	ENSLAFG00000020514	2 retrocopies	retro_lafr_1071, retro_lafr_903,
Macropus eugenii	ENSMEUG00000000315	1 retrocopy	retro_meug_247,
Mus musculus	ENSMUSG00000028647	1 retrocopy	retro_mmus_1626 ,
Nomascus leucogenys	ENSNLEG00000011814	2 retrocopies	retro_nleu_1319, retro_nleu_2489,
Oryctolagus cuniculus	ENSOCUG00000022203	2 retrocopies	retro_ocun_907, retro_ocun_979,
Otolemur garnettii	ENSOGAG00000024435	3 retrocopies	retro_ogar_1283, retro_ogar_1553, retro_ogar_1880,
Pongo abelii	ENSPPYG00000001515	1 retrocopy	retro_pabe_1400,
Pan troglodytes	ENSPTRG00000000565	2 retrocopies	retro_ptro_1120, retro_ptro_1594,
Rattus norvegicus	ENSRNOG00000017166	2 retrocopies	retro_rnor_573, retro_rnor_779,
Sus scrofa	ENSSSCG00000003649	2 retrocopies	retro_sscr_1176, retro_sscr_1217,
Ictidomys tridecemlineatus	ENSSTOG00000021547	2 retrocopies	retro_itri_1518, retro_itri_252,
Tarsius syrichta	ENSTSYG00000005690	1 retrocopy	retro_tsyr_172,
Tursiops truncatus	ENSTTRG00000009583	1 retrocopy	retro_ttru_1872,