RetrogeneDB ID: retro_mmur_400

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2839:56605..57426(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT52
• Ensembl ID: ENSMICG00000015182
• Aliases: None
• Description: intraflagellar transport 52 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:15901]

Sequence

>retro_mmur_400
GCTCTCACCTTTGTCTATCATTTTGGTGCCACATGAAGTTTCATGAAACCTGCAGTGGCTGTTCTGTCTACGGGCTCTGT
CTACTTTCAACTTAACAGAAGCATTCTGGCTTTCTATTACTCAAAGAGCCAAGGTGAGAAGCTGGCAGTGCTTGGCTCAT
GTCACATGTTCACTGACCAATATTTGGATAAAGAAGAAAACAGCAAAATCATGGATGTTGTTTTCCAGTGGTTCATGACA
GAAGATATCCAACTAAACCAGATTGATGCTGACGACCCTGAGATGTCAGACTACATGATGCTGCCTGACACAGCCACCCT
GTCAGAGCAACTTCGAGTGTGTCTCCAGGAGGGCAAGGGGAACCCTTGGGACTTCACCACCCTCTTTGACTTGTCCATTT
ACCAGCGGGATACCACCTCCTCCTGCAAGGTCATCAAGGCTCATGAGCAGCTAAACCTGAAACATGAACCACTCCAGCTC
ATCCAAGCTCAGTTTGAGACACCACTGCCAGCCTTCAGCCTGCAGTTTTCCCGCCTAGTTTCAGGGAATTACCACTTCCT
CCTCTGGAGCTGTTTGGCTAAGATGAAACGTTCTCCTCTGAGAAGGTACAGCTTGCTCAGATTACCAATAAGTGTACAGG
AGAAGACCTGGAATTCTATGTCAGGAAGTGTGGTGATATTCTTGGAGTAACCAGTAAACTACCAAAGGACCAACAAGGTG
CCAAAGCTAACCTTGAGCACATCTTCTTCCAAGTGGTGGAGTTCAAGAAATTGAACCAGGAACATGACATTGACAGAAGT
AAAACAGCATTCCAGAACAAT

Alignment

ORF - retro_mmur_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.82 %
• Parental protein coverage: 62.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALTFVYPFGATLSVMKPAVAVLSTGSVCFPLNRPILAFYHSKNQGGKLAVLGSCHMFSDQYLDKEENSKI
          ALTFVY.FGAT.S.MKPAVAVLSTGSV.F.LNR.ILAFY.SK.QG.KLAVLGSCHMF.DQYLDKEENSKI
Retrocopy ALTFVYHFGAT*SFMKPAVAVLSTGSVYFQLNRSILAFYYSKSQGEKLAVLGSCHMFTDQYLDKEENSKI

Parental  MDVVFQWLTTEDIHLNQIDAEDPEISDYMMLPDTASLSERLRVCLQEGDENPRDFTTLFDLSIYQLDTTS
          MDVVFQW..TEDI.LNQIDA.DPE.SDYMMLPDTA.LSE.LRVCLQEG..NP.DFTTLFDLSIYQ.DTTS
Retrocopy MDVVFQWFMTEDIQLNQIDADDPEMSDYMMLPDTATLSEQLRVCLQEGKGNPWDFTTLFDLSIYQRDTTS

Parental  LPKVIKAHEQLNVKHEPLQLIQPQFETPLPA-LQPAVFPPSFRELPPPPLELFDLDETFSSEKARLAQIT
          ..KVIKAHEQLN.KHEPLQLIQ.QFETPLPA.LQPAVFPPSFRELP.PPLELF..DETFSSEK..LAQIT
Retrocopy SCKVIKAHEQLNLKHEPLQLIQAQFETPLPA<LQPAVFPPSFRELPLPPLELFG*DETFSSEKVQLAQIT

Parental  NKCTEEDLEFYVRKCGDILGVTSKLPKDQQDAKHILEHIFFQVVEFKKLNQEHDIDTSEMAFQSN
          NKCT.EDLEFYVRKCGDILGVTSKLPKDQQ.AK..LEHIFFQVVEFKKLNQEHDID.S..AFQ.N
Retrocopy NKCTGEDLEFYVRKCGDILGVTSKLPKDQQGAKANLEHIFFQVVEFKKLNQEHDIDRSKTAFQNN

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_400 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_400 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027175	1 retrocopy	retro_cpor_301,
Microcebus murinus	ENSMICG00000015182	1 retrocopy	retro_mmur_400 ,
Myotis lucifugus	ENSMLUG00000016664	1 retrocopy	retro_mluc_990,
Otolemur garnettii	ENSOGAG00000007699	1 retrocopy	retro_ogar_2343,
Takifugu rubripes	ENSTRUG00000014953	1 retrocopy	retro_trub_46,