RetrogeneDB ID: retro_mmur_1603

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_9107:49067..50020(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSMICG00000017145
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_mmur_1603
AAGGAAAATTTTAATATGTGTGATAACTTGAAAGATGGTGAAAAACATCCAATCCTTAATCCTACATGTACATTTGCTGA
TGCCTTTCTATGTTACCCTGAAATTTTAGAAACCATTAAAAAGGCTTTTGAAAACCTGCCAACACCTATTCAGTCACAAT
CGTGGCCAATAGTTCTATAAGGAATAGACCTTATAGGAATAGCCCAAACAGGAACAGGAAAGACATTGTCCTATTTAATG
CCTGGATTTATTCATGTAGACGGTCAACCACAAGTTAGAGAAAAAGAGGAAGACCCAGTATGTTAGTTCTCACACCCACT
CGTGAATTAGCTATTCAAGTGGAATTTGAATGTCCTAAATATTCATATAAAGGACTTAAGAGTGTTTGTACATATGGTGG
TGGAAATAGAGACCAACAAATAGAAGATCTTAGAAAAGGTATACATATCGTCATTGTAACACCTGGAAGGTTGAATGATC
TGCAAATGAATAACTTTGTCAACTTTGAAAAGCGTAACCTACTTGGTTTTGGATGAAGCAGACAAAATGCTTGATATGGG
ATTTGAACCCCAGATTATGAAGATTTTGTTAGATGTGTGCCCAGATAGGCAGACTATTATGACAAGTACAACTTGGCCAT
GTGCTGTTAGGCGACTCGCACAGTCTTGTTTGAAAACACCAATGATTGTCTATGTTGGAACGTTGGACCTTGTAGCTGTG
AGCCCAGTAGAACAGAGTGCAATTGTCACAACAGAAGAAAAACGAGGTCACATCCAAACATTTCTAGAGCATTTGTCGTC
CAACGACAAAGTCATTGTCTTTGTTTGCCGAAAAGCCGTTGCGGATCATTTATCCAGTGACCTGATTCTCTGACATATCA
GTAGAATCATTACATGGCAACAGAGAACAGGGGGACAGAGAAAAGGCTTTAAGAAGATTTTAAAACAGGAAAA

Alignment

ORF - retro_mmur_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.45 %
• Parental protein coverage: 52.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KENFNIMCDDLKDGEKRPIPNPTCTFADAFQCYPEILETIKKAGFQKPTPIQSQSWPIVLQGIDLIGIAQ
          KENFN.MCD.LKDGEK.PI.NPTCTFADAF.CYPEILETIKKA....PTPIQSQSWPIVL.GIDLIGIAQ
Retrocopy KENFN-MCDNLKDGEKHPILNPTCTFADAFLCYPEILETIKKAFENLPTPIQSQSWPIVL*GIDLIGIAQ

Parental  TGTGKTLSYLMPGFIHLDGQPKVR-GKRGRPGMLVLTPTRELAIQVEFECSKYSYKGL-SVCIYGGGNRD
          TGTGKTLSYLMPGFIH.DGQP.VR..KRGRP.MLVLTPTRELAIQVEFEC.KYSYKGL.SVC.YGGGNRD
Retrocopy TGTGKTLSYLMPGFIHVDGQPQVR<RKRGRPSMLVLTPTRELAIQVEFECPKYSYKGLKSVCTYGGGNRD

Parental  QQIEDLRKGVDIVIATPGRLNDLQMNNFVN-LKSITYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTIM
          QQIEDLRKG..IVI.TPGRLNDLQMNNFVN.LKS.TYLVLDEADKMLDMGFEPQIMKILLDV.PDRQTIM
Retrocopy QQIEDLRKGIHIVIVTPGRLNDLQMNNFVN>LKSVTYLVLDEADKMLDMGFEPQIMKILLDVCPDRQTIM

Parental  TSATWPCAVRRLAQSYLKTPMIVYVGTLDLVAVSTVEQSVIVTTEEEKRGHIQTFLEHLSPNDKVIVFVC
          TS.TWPCAVRRLAQS.LKTPMIVYVGTLDLVAVS.VEQS.IVTT.EEKRGHIQTFLEHLS.NDKVIVFVC
Retrocopy TSTTWPCAVRRLAQSCLKTPMIVYVGTLDLVAVSPVEQSAIVTT-EEKRGHIQTFLEHLSSNDKVIVFVC

Parental  RKAVADHLSSDLILRHISVESLHGNREQGDR-EKALRDFKTGK
          RKAVADHLSSDLIL.HIS.......R..G.R......DFKTGK
Retrocopy RKAVADHLSSDLIL*HISRIITWQQRTGGQR<KRL*EDFKTGK

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_1603 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1603 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 16 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603 ,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,