RetrogeneDB ID: retro_mmur_344

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2510:24394..25436(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT4
• Ensembl ID: ENSMICG00000015263
• Aliases: None
• Description: chaperonin containing TCP1, subunit 4 (delta) [Source:HGNC Symbol;Acc:1617]

Sequence

>retro_mmur_344
TCCACTTCCAAAACTGTTGCTGATGCTATTATAACAAGACTTGGACCAAAAGGAAAGGACAAAACAAGTCAAAATGGAAA
CATTATATGAGCATTACAAATATTACTGCCACCAGTCTGAAAAAAAATACAAGTGTTACATGCAGAAGCCAGAATGCTGG
TGGAACTGTCTAAGGCTTAAGATATAGAAGCAGGAAATGACACCACATCAGTGATCATCATTGCTGGCTCTCAGATTCCT
GTAACTAGCTTCTTCAGAATGGGATTCATCCAACCAATATTTCAGAGTCATTCCAGAAGGGTTTGGAAAGGGTATTAAAA
TTTTAATTAACATGTCTTGATCTATCGAACTGAGTTACAGAGAAACTTTGTTAAAGAGTACTACCACATCATTGAACTCA
AAGGTTATCTTTCAACATTGAAGTCTACTTTCTCCAATAAATGTAAATACAATACTTAAAGTGGTTGCTCTAGCCACAGC
TACCAGTGTAGATCTTAGGAGATTTTTAAATGGTTAAGAAATTTGGTGGGACAATTGATGACTATGAGGTGGCACAAGGG
CTGGTTCTCACCCAAAAGGTAGCAAAATATGGCATAGCCAGAGTTGAAAAGGCTAAAATTGGGCTTATTCAGTTTTGCTT
ATTTGCTCCTAAAACAGATATGTATAATTAAATAATTTCTGACTTACCCAGATGGACCAAATGCTCTGAGAGTAAAGAGC
CTGTAAGCTAAATTTAATAAAGTAAAATTTTAAAACAGGATGTAATGTCCTCCTCATACAGAAGTGCATTCTAGGGGATG
CTCTTGGTCATTTTGTGTTACATTTTCTAAACAAAGTGAATATTATGGCAATTAGGGATATTGAAAGAGAAGACATTCAA
TTTATTTGTAAAACAATTGGAAACAAGCCAGTAGCTCATATTCACCAATTCACTGCTGATATACTGAGTTCTTGCCAGTT
ATCCAAGGATGTCAGTATAAATGGTTCTGGCAAATTACCCAAGATTTAAGGCTGTGCAAGCCCTGGGTAAAAAGTTACAG
TT

Alignment

ORF - retro_mmur_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.85 %
• Parental protein coverage: 64.94 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SAAKAVADAIRTSLGPKGMDKMIQDG-KGDVTITNDGATILKQM-QVLHPAARMLVELSKAQDIEAGDGT
          S..K.VADAI.T.LGPKG.DK..Q.G.K....ITN..AT.L....QVLH..ARMLVELSKA.DIEAG..T
Retrocopy STSKTVADAIITRLGPKGKDKTSQNG<KHYMSITNITATSLXXX>QVLHAEARMLVELSKA*DIEAGNDT

Parental  TSVVIIAGS-LLDSCTKLLQKGIHPTIISESFQKALE-KGVEVLTDMSRPVELSDRETLLNSATTSLNSK
          TS.VII....L.DSC..LLQ.GIHPT.ISESFQK.LE.KG...L..MS...ELS.RETLL.S.TTSLNSK
Retrocopy TS-VIIIAG<LSDSCN*LLQNGIHPTNISESFQKGLE<KGIKILINMS*SIELSYRETLLKSTTTSLNSK

Parental  VVSQYSSLLSPMSVNAVMKVIDPATATSVDLR-DIKIVKKLGGTIDDCELVEGLVLTQKVANSGITRVEK
          V..Q..SLLSP..VN...KV...ATATSVDLR.D...VKK.GGTIDD.E...GLVLTQKVA..GI.RVEK
Retrocopy VIFQH*SLLSPINVNTILKVVALATATSVDLR>DF*MVKKFGGTIDDYEVAQGLVLTQKVAKYGIARVEK

Parental  AKIGLIQFCLSAPKTDMDNQIVVSDY-AQMDRVLREERAYILNLVKQIKKTGCNVLLIQKSILRDALSDL
          AKIGLIQFCL.APKTDM.N.I..SD...QMD..L.E.RA..LNL.K...KTGCNVLLIQK.IL.DAL...
Retrocopy AKIGLIQFCLFAPKTDMYN*II-SDL<TQMDQML*E*RACKLNLIK*NFKTGCNVLLIQKCILGDALGHF

Parental  ALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHIDQFTADMLGSAELAEEVNLNGSGKLLKITGCASP
          .LHFLNK..IM.I.DIEREDI.FICKTIG.KPVAHI.QFTAD.L.S..L...V..NGSGKL.KI.GCASP
Retrocopy VLHFLNKVNIMAIRDIEREDIQFICKTIGNKPVAHIHQFTADILSSCQLSKDVSINGSGKLPKI*GCASP

Parental  GKTVTI
          G..VT.
Retrocopy G*KVTV

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_344 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_344 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003083	2 retrocopies	retro_cfam_2093, retro_cfam_590,
Callithrix jacchus	ENSCJAG00000008703	1 retrocopy	retro_cjac_724,
Equus caballus	ENSECAG00000016982	1 retrocopy	retro_ecab_148,
Microcebus murinus	ENSMICG00000015263	1 retrocopy	retro_mmur_344 ,
Macaca mulatta	ENSMMUG00000013973	1 retrocopy	retro_mmul_2500,
Monodelphis domestica	ENSMODG00000002882	1 retrocopy	retro_mdom_1402,
Otolemur garnettii	ENSOGAG00000003974	2 retrocopies	retro_ogar_1041, retro_ogar_1931,
Sorex araneus	ENSSARG00000010539	1 retrocopy	retro_sara_7,