RetrogeneDB ID: retro_mmus_1539

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:3155859..3156365(+)
• Located in intron of: ENSMUSG00000046201

Retrocopy information

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

Parental gene information

• Parental gene symbol: Myl12b
• Ensembl ID: ENSMUSG00000034868
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:MGI Symbol;Acc:MGI:107494]

Sequence

>retro_mmus_1539
CGAGCAAAAAAGTGAAGACCAGGACCACCAAGAAGCACCCTCAGAGCGTCCAATGTGTTCTCCATGTTTGACCAGTCCCA
GATCCAGGAGTTCAAAGAGGCCTTTAACATGATTGACCAGAACTGGGATGGCTTCATTGACAAGGAGGACCTGCACGACA
TGCTGGCATCTCTGGGAAGAACCCCACTGATACCTACCTGGACGCCATGATAAACGAGGCCCTGAGCCCCATCAATTTCA
CCATGTTCCTCACAATGTTTGGAGAGAAACTGAATGGAACTGACCCCAAGGACGTCATCAGAAACGCCTTTTCTTGCTTC
GATGAGGAAGCCACAGGCACCATCCAGGAGGATTACCTGAGGGAGCTGCTGACCACCATGGGCGACCGCTTCACAGACAA
GGAAGTGGATGAGCTGTACAGAGAGGCCCCCATTGACAAAAAGGGGAACTTCAACTACGTTGAGTTCACACGTATCCTGA
AGCACGGAGCAAAAGACAAAGATGAC

Alignment

ORF - retro_mmus_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 96.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTKTTKKRPQRAT---SNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLG-KNPTDAYLDA
          ..K.....P.R.T...SNVF.MFDQSQIQEFKEAFNMIDQN.DGFIDKEDLHDMLASLG.KNPTD.YLDA
Retrocopy RAKK*RPGPPRSTLRASNVFSMFDQSQIQEFKEAFNMIDQNWDGFIDKEDLHDMLASLG<KNPTDTYLDA

Parental  MMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEVDEL
          M.NEA..PINFTMFLTMFGEKLNGTDP.DVIRNAF.CFDEEATGTIQEDYLRELLTTMGDRFTD.EVDEL
Retrocopy MINEALSPINFTMFLTMFGEKLNGTDPKDVIRNAFSCFDEEATGTIQEDYLRELLTTMGDRFTDKEVDEL

Parental  YREAPIDKKGNFNYIEFTRILKHGAKDKDD
          YREAPIDKKGNFNY.EFTRILKHGAKDKDD
Retrocopy YREAPIDKKGNFNYVEFTRILKHGAKDKDD

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	0.19 RPM	109.92 RPM
SRP007412_cerebellum	0.13 RPM	68.13 RPM
SRP007412_heart	0.12 RPM	28.02 RPM
SRP007412_kidney	0.17 RPM	70.05 RPM
SRP007412_liver	0.08 RPM	37.33 RPM
SRP007412_testis	1.05 RPM	16.51 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_1539 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	17:3155879..3156508
ENCFF001YIJ	POLR2A	17:3154212..3155466

EST

No EST(s) were mapped for retro_mmus_1539 retrocopy.

TSS

No TSS is located nearby retro_mmus_1539 retrocopy 5' end.

Lab

retro_mmus_1539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1539 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012665	1 retrocopy	retro_amel_1847,
Canis familiaris	ENSCAFG00000032168	1 retrocopy	retro_cfam_1224,
Dasypus novemcinctus	ENSDNOG00000007004	2 retrocopies	retro_dnov_463, retro_dnov_953,
Dipodomys ordii	ENSDORG00000007562	1 retrocopy	retro_dord_531,
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311,
Felis catus	ENSFCAG00000022871	1 retrocopy	retro_fcat_2019,
Homo sapiens	ENSG00000118680	4 retrocopies	retro_hsap_1487, retro_hsap_3129, retro_hsap_3451, retro_hsap_3985,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Myotis lucifugus	ENSMLUG00000005189	2 retrocopies	retro_mluc_706, retro_mluc_947,
Monodelphis domestica	ENSMODG00000021464	1 retrocopy	retro_mdom_987,
Mustela putorius furo	ENSMPUG00000005011	1 retrocopy	retro_mputfur_294,
Mus musculus	ENSMUSG00000024048	1 retrocopy	retro_mmus_1149,
Mus musculus	ENSMUSG00000034868	2 retrocopies	retro_mmus_1483, retro_mmus_1539 ,
Nomascus leucogenys	ENSNLEG00000006907	3 retrocopies	retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Otolemur garnettii	ENSOGAG00000029777	2 retrocopies	retro_ogar_2409, retro_ogar_857,
Pongo abelii	ENSPPYG00000009032	3 retrocopies	retro_pabe_1236, retro_pabe_2585, retro_pabe_3026,
Pan troglodytes	ENSPTRG00000009836	4 retrocopies	retro_ptro_1006, retro_ptro_2118, retro_ptro_2340, retro_ptro_2705,
Rattus norvegicus	ENSRNOG00000015733	2 retrocopies	retro_rnor_1614, retro_rnor_2718,
Tarsius syrichta	ENSTSYG00000010418	9 retrocopies	retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,