RetrogeneDB ID: retro_rnor_1614

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:66962403..66962888(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022100
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Myl12b
• Ensembl ID: ENSRNOG00000015733
• Aliases: Myl12b, Mrlc2, Mrlcb, Mylc2b
• Description: Myosin regulatory light chain 12B [Source:UniProtKB/Swiss-Prot;Acc:P18666]

Sequence

>retro_rnor_1614
AGGGCGAAGACCAAGGCCACTAAGGACCACGTCAGAGCACAACATCCACTGTGTTTGCTCAACAAAACACAGAACCAGAA
ATTCAAAAAGGGTTTCACATGACTAACTGTGGCAGGGATGGCTTCATTTACAAGGCCAACTTGCTTCCCTCACTGAGGGG
GATTGCCAACAGAATCTCTCGATGTCATGGTGAGTGAAGCTCCAGGCTCCATTGATTTTACTATATTCCTCCCTGAAGAC
AGTGAGAAGTTGAAGGGTACAGATCCTGAAGATATTATCAGAAATGCATTTGCCCGCGTTGATGAAGAAGACCCTGGCAC
CATCCAGGAAGAACGCCTGAGAGATCTGCTGACTACCACAAGTGATGAGTTTACAGATGGGGAAGTCAATGAACTGTTCA
AGGAAGACCATATTGACAAAGAGGGGAAATCAGCTATAGTGAGTTCTCCAACATCCGTCAATGTGGATCAAAAGGCACAG
ATGAC

Alignment

ORF - retro_rnor_1614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KAKTKTTKKRP-QRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASL-GKNPTDAYLDA
          .AKTK.TK....Q..TS.VFA...Q....E....F.M....RDGFI.K......L.SL.G..PT...LD.
Retrocopy RAKTKATKDHV<QSTTSTVFAQ--QNTEPEIQKGFHMTNCGRDGFIYKAN---LLPSL>GGLPTES-LDV

Parental  MMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEVDEL
          M..EAPG.I.FT.FL....EKL.GTDPED.IRNAFA..DEE..GTIQE..LR.LLTT..D.FTD.EV.EL
Retrocopy MVSEAPGSIDFTIFLPEDSEKLKGTDPEDIIRNAFARVDEEDPGTIQEERLRDLLTTTSDEFTDGEVNEL

Parental  YREAPIDK-KGNFNYIEFTRILKHGAKDKDD
          ..E..IDK..G...Y.EF..I...G.K..DD
Retrocopy FKEDHIDK<RGEISYSEFSNIRQCGSKGTDD

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
SRP017611_brain	0.00 RPM	135.24 RPM
SRP017611_kidney	0.00 RPM	143.61 RPM
SRP017611_liver	0.00 RPM	47.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1614 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1614 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1614 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1149

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 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	ENSMUSG00000034868	2 retrocopies	retro_mmus_1483, retro_mmus_1539,
Nomascus leucogenys	ENSNLEG00000006907	3 retrocopies	retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Oryctolagus cuniculus	ENSOCUG00000021304	1 retrocopy	retro_ocun_900,
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,
Tupaia belangeri	ENSTBEG00000009299	4 retrocopies	retro_tbel_1294, retro_tbel_1629, retro_tbel_3088, retro_tbel_3438,
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,