RetrogeneDB ID: retro_mmur_606

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_4154:420948..421562(-)
• Located in intron of: ENSMICG00000006444

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSMICG00000016266
• Aliases: None
• Description: zinc finger, CCHC domain containing 9 [Source:HGNC Symbol;Acc:25424]

Sequence

>retro_mmur_606
GAGTACTTAAATGAAGATGTGAATGGATTCATGGAATACCTAAGACAGAGCTCACAGATGGTTCACAATGGGGAGATTAT
AGCAATAGAAGTTCAGAAAGTAAGGGAAGAAATTGCAGTTGCTTTCAAGAAAGACAGTCGATGGGAAGGAAGGTGATTAA
AAAGATGAGCAGCAAAGAAAAATGCAATGGTATGTTTCTACTGCAGAACCTGGTTATGGAATTGCAGATTGCCCAGCCAC
CCTTGAAAACCAAGATATGGGGCCGGAATGTGTTACTGGGGTAGGTCCCTGGAGCATGAAATAACCATGTATAAGGCTAA
AGTAGACCCAGCTCTTGGTGAATTTCCTTTTGCAAGATGTTTTGCTTGTGAGGAAATGGGACACCTGTCTACATCTTCTC
CCGATAATCCCAAAGGACTCTATGCTGATGGTGGTGGTTGCAAACGTTGTGGCTCTGTGGAACATTTTAAGAAAGATTGC
CCTGAAGGTTAGAATTCAGATTGAATGGTCACAGTTGGTTGCTGGCAAAGGGACTGAGTGCAGAGTATGAAGACACTTTG
GATGCACCTAAACCGCAGAAACCCCAAACAAAGAAACTTAAAATGGTTAATTTT

Alignment

ORF - retro_mmur_606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.48 %
• Parental protein coverage: 76.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EYFNEDVNGFMEYLRQNSQMVHNGDIIATDNQEVREEIAVALKKDSRREGRRL-KRQAAKKNAMVCFHCR
          EY.NEDVNGFMEYLRQ.SQMVHNG.IIA...Q.VREEIAVA.KKDSR.EGR.L.K....K......F...
Retrocopy EYLNEDVNGFMEYLRQSSQMVHNGEIIAIEVQKVREEIAVAFKKDSRWEGR*L<KKMSSKEKCNGMFLLQ

Parental  -KPGHGIADCPAALENQDMG-TGICYRCGSTEHEITKCKAKVDPAVGEFPFAKCFVCGEMGHLSRSCPDN
          ..PG.GIADCPA.LENQDMG..G.CY...S.EHEIT..KAKVDPA.GEFPFA.CF.C.EMGHLS.S.PDN
Retrocopy <EPGYGIADCPATLENQDMG<AGMCYWGRSLEHEITMYKAKVDPALGEFPFARCFACEEMGHLSTSSPDN

Parental  PKGVYADGGGCKLCGSVKHFKKDCPESQNSDQMVTVGRW-SKGMSADYEEILDAPKPPKPKAKIPKIVNF
          PKG.YADGGGCK.CGSV.HFKKDCPE..NSD.MVTVG.W..KG.SA.YE..LDAPKP.KP..K..K.VNF
Retrocopy PKGLYADGGGCKRCGSVEHFKKDCPEG*NSD*MVTVGCW<AKGLSAEYEDTLDAPKPQKPQTKKLKMVNF

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_606 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_606 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 15 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Microcebus murinus	ENSMICG00000016266	5 retrocopies	retro_mmur_125, retro_mmur_1325, retro_mmur_1341, retro_mmur_606 , retro_mmur_819,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tarsius syrichta	ENSTSYG00000012423	1 retrocopy	retro_tsyr_244,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,