RetrogeneDB ID: retro_mmus_1149

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:116361197..116361694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Myl12a
• Ensembl ID: ENSMUSG00000024048
• Aliases: Myl12a, 2900073G15Rik, AI838292, C80200
• Description: myosin, light chain 12A, regulatory, non-sarcomeric [Source:MGI Symbol;Acc:MGI:1914518]

Sequence

>retro_mmus_1149
AGGGCAAAGACCAAGGCCACTAACAATCACCTCAGTGTACCACATCCACTGTGTTTGCTCTGCTTCACAAAACACAGATA
CAGAAATTCAAATAGGGCTGCCACATGACTGACTGTGACAGGAATGGCTTCATCTACAAGGAAGACTTGCTTCCCTCACT
GGGGGGAATTCCAATTGAAGAATATCTGGATATTGTGATGAGTGAGGCTCTAGGTCCCATTGATTTCATCATATACCTCC
CTGTAATCAGCAAGAAGTTGAAGAGTCTAGATTCTGAAGATATTACCAGAAATGTATTTGCCTGCTATGATGAAGAAGCT
GCTGGTACCATCCAGGAAGAACACCTGAGAGATCTGCTGAGTACCACAAATGATGAGTTTACAGATGGGGGAGTCGATGA
GCTAGCTGCTCAGGGAAGATCATGTTGACAAAGAGGGAAAGTCAATTATAGTGAGTTCTCACACAATCTTAAACATGGAT
CAAAAGGCATAGATGAC

Alignment

ORF - retro_mmus_1149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.18 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RAKTKTTKKR-PQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASMGKNPTDEYLDAM
          RAKTK.T....PQ..TS.VFA.....QIQ.FK....M.D..R.GFI.KE...D.L.S.G..P..EYLD..
Retrocopy RAKTKATNNH<PQCTTSTVFALLHKTQIQKFK*GCHMTDCDRNGFIYKE---DLLPSLGGIPIEEYLDIV

Parental  MNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEAIGTIQEDYLRELLTTMGDRFTDEEVDELY
          M.EA.GPI.F...L.....KL...D.ED..RN.FAC.DEEA.GTIQE..LR.LL.T..D.FTD..VDEL.
Retrocopy MSEALGPIDFIIYLPVISKKLKSLDSEDITRNVFACYDEEAAGTIQEEHLRDLLSTTNDEFTDGGVDELA

Parental  REA-PIDKKGNFNYIEFTRILKHGAKDKDD
          .........G..NY.EF...LKHG.K..DD
Retrocopy AQGRSC*QRGKVNYSEFSHNLKHGSKGIDD

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	14.88 RPM
SRP007412_cerebellum	0.00 RPM	20.80 RPM
SRP007412_heart	0.00 RPM	306.57 RPM
SRP007412_kidney	0.00 RPM	145.12 RPM
SRP007412_liver	0.00 RPM	40.01 RPM
SRP007412_testis	0.00 RPM	17.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1149 was not detected

EST

No EST(s) were mapped for retro_mmus_1149 retrocopy.

TSS

No TSS is located nearby retro_mmus_1149 retrocopy 5' end.

Lab

retro_mmus_1149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1149 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1614

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016024	2 retrocopies	retro_btau_1273, retro_btau_1693,
Canis familiaris	ENSCAFG00000029134	3 retrocopies	retro_cfam_166, retro_cfam_583, retro_cfam_79,
Choloepus hoffmanni	ENSCHOG00000005206	54 retrocopies	retro_chof_1002, retro_chof_1149, retro_chof_1238, retro_chof_1250, retro_chof_1273, retro_chof_1321, retro_chof_1326, retro_chof_135, retro_chof_1352, retro_chof_1363, retro_chof_1374, retro_chof_1439, retro_chof_1505, retro_chof_1520, retro_chof_1538, retro_chof_1553, retro_chof_1574, retro_chof_1594, retro_chof_1608, retro_chof_1641, retro_chof_1694, retro_chof_1783, retro_chof_1790, retro_chof_1798, retro_chof_1801, retro_chof_1804, retro_chof_1809, retro_chof_1875, retro_chof_1879, retro_chof_1887, retro_chof_2059, retro_chof_2114, retro_chof_2157, retro_chof_2180, retro_chof_2353, retro_chof_2430, retro_chof_2492, retro_chof_2510, retro_chof_2516, retro_chof_2597, retro_chof_2638, retro_chof_2639, retro_chof_2689, retro_chof_543, retro_chof_545, retro_chof_584, retro_chof_606, retro_chof_618, retro_chof_667, retro_chof_686, retro_chof_696, retro_chof_729, retro_chof_752, retro_chof_949,
Callithrix jacchus	ENSCJAG00000038151	2 retrocopies	retro_cjac_1279, retro_cjac_3119,
Echinops telfairi	ENSETEG00000011271	3 retrocopies	retro_etel_393, retro_etel_439, retro_etel_96,
Microcebus murinus	ENSMICG00000017884	2 retrocopies	retro_mmur_1194, retro_mmur_1585,
Mus musculus	ENSMUSG00000024048	1 retrocopy	retro_mmus_1149 ,
Mus musculus	ENSMUSG00000034868	2 retrocopies	retro_mmus_1483, retro_mmus_1539,
Otolemur garnettii	ENSOGAG00000001340	7 retrocopies	retro_ogar_1877, retro_ogar_2516, retro_ogar_2536, retro_ogar_2540, retro_ogar_347, retro_ogar_517, retro_ogar_605,
Sorex araneus	ENSSARG00000011512	1 retrocopy	retro_sara_102,
Ictidomys tridecemlineatus	ENSSTOG00000027658	2 retrocopies	retro_itri_1480, retro_itri_896,