RetrogeneDB ID: retro_mmur_1562

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_832:297397..298559(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSMICG00000015780
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_mmur_1562
ATGGAAACTGAATAGCCAGAGGGAAACCTTCCCCAACACTGAAACCAATGGTGAATTTGGTAAACGCCCTGCAGAAGATA
TGGAAGAGGAACAAACATTAAAAGGTCTAGAAACACTGATGAGATGGTAGAATTACGCATTCTGCTTCAGAGCAAGAATG
CTGGGGCAGTGGTTGGAAAAGGAGGCAAGAATATTAAGGCTCTCCGTACTGACTACAATGCCAGTGTTTCAGTCCCAGAC
AGCAGTGGCCCTGAGCGCACATTGAGTATCAGTGCTGATATTGAAACAATTGGAGAAATTCTGAAGAAAATCATCCCTAC
CTTGGAAGAGGGCCTGCAGTTGTCATCACCCACGGCAACCAGCCAGCTCCCGCTCGAATCTGATGCTAGTGGAATGCTTA
AATTACCAGCACTATAAAGGAAGCGACTTTGACTGCAGAGTTGAGACTGTTGATTCATCAGAGTCTGTCGGGAGGAATTA
TTGGGGTCAAAGGTGCTAAAATCAAAGAACTTCGTGAGACACTCAAACAACAATCAAGCTTTTCCAGGAATGCTGTCCTC
ATTCCACTGACAGAGTCATTCTTATTGGAGGAAAACCTGATAGGGTTGTAGAGTGCATAAAGATCATTCTCAATCTTATA
TCTGAGTCTCCCATCAAAGGACGTGCACAGCCTTATGATCCCAATTTTTACGATGAAACTTATGATTATGGTGGTTTTAC
AATGATGTTTGGTGACCGCTGTGGAAGGCCTGTAGGATTTCCAATGTGGGGAAGAGGTGATTTTGACAGAATGCCTCCTG
GTCAGGGTGGGCGTCCCATGCCTCCGTCTAGAAGAGATTATGATGATATGAGCCCTCGTGGAGGACCACCTCCCCCTCCT
CCTGGTAGAGGTGGCTGGGGTGGTAGTAGAGCTCAGAATCTCCCTCTTCCTCCTTCACCACCTCCTGGAGGAGGAGATCT
AATTGCCTATGATAGAAGAGGAAGACCTGGAGACCGCTACGATGGCATGGTTGGTTTCAGTGCTGATGAAACTTGGGACT
CTGCAGTAGATACATGGAGCCCATCAGAATGGCAGATGGCTTATGAACCACAGGGAGGCTCTGGATATGATTATTCCTAT
GCAGGGGGTCGTGGCTCATATGGTGATCTTGGTGGACCTATT

Alignment

ORF - retro_mmur_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  METEQPE-ETFPNTETNGEFGKRPAEDMEEEQAFK-RSRNTDEMVELRILLQSKNAGAVIGKGGKNIKAL
          METE.PE.ETFPNTETNGEFGKRPAEDMEEEQ..K.RSRNTDEMVELRILLQSKNAGAV.GKGGKNIKAL
Retrocopy METE*PE>ETFPNTETNGEFGKRPAEDMEEEQTLK<RSRNTDEMVELRILLQSKNAGAVVGKGGKNIKAL

Parental  RTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLXXGLQLPSPNATSQLPLESDA-VECLNYQH
          RTDYNASVSVPDSSGPER.LSISADIETIGEILKKIIPTL..GLQL.SP.ATSQLPLESDA.VECLNYQH
Retrocopy RTDYNASVSVPDSSGPERTLSISADIETIGEILKKIIPTLEEGLQLSSPTATSQLPLESDA>VECLNYQH

Parental  YKGSDFDC-ELRLLIHQSLAGGIIGVKGAKIKELRE-NTQTTIKLFQECCPHSTDRVVLIGGKPDRVVEC
          YKGSDFDC.ELRLLIHQSL.GGIIGVKGAKIKELRE..TQTTIKLFQECCPHSTDRV.LIGGKPDRVVEC
Retrocopy YKGSDFDC>ELRLLIHQSLSGGIIGVKGAKIKELRE<DTQTTIKLFQECCPHSTDRVILIGGKPDRVVEC

Parental  IKIILDLISESPIRAQ---YDP-FYDE---YDVFTMMFDD--GR-VGFPMRRGGD--RMPPGRGGR-MPP
          IKIIL.LISESPI......YDP.FYDE...Y..FTMMF.D..GR.VGFPM...GD..RMPPG.GGR.MPP
Retrocopy IKIILNLISESPIKGRAQPYDPNFYDETYDYGGFTMMFGDRCGRPVGFPMWGRGDFDRMPPGQGGRPMPP

Parental  SRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETW
          SRRDYDDMSPR.GPPPPPPGRGG.GGSRA.NLPLPP.PPP.GGDL.AYDRRGRPGDRYDGMVGFSADETW
Retrocopy SRRDYDDMSPRGGPPPPPPGRGGWGGSRAQNLPLPPSPPPGGGDLIAYDRRGRPGDRYDGMVGFSADETW

Parental  DSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPI
          DSA.DTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPI
Retrocopy DSAVDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1562 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1562 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562 , retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,