RetrogeneDB ID: retro_mmur_1121

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_23821:8019..8385(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSMICG00000000349
• Aliases: None
• Description: prefoldin subunit 1 [Source:HGNC Symbol;Acc:8866]

Sequence

>retro_mmur_1121
ATGGCGGCCCCCGTGGATCTGGAGTTGAAAAAGGCCTTCACAGAGCTTCAAGCCAAAGTTATTGACACTCAACAGAAGGT
GAAGCTTGCAGACATACAGATTGAACAGCTGAACAGAACGAAAAAGCATGCACATCTTACAGATACAGAGATTATGACTT
TGGTAGATGAAACTAACATGTATGAAGGTGTAGGAAGAATGTTTATTCTTCAATCCAAGGAGGTAATTCACAATCAGCTG
TTAGAGAAACAGAGAATAGCAGAAGACAAAATAAAAGAATTAGAACAGAAAAAATCCTACCTGGAACGGAGCGTTAAGGA
AGCTGAAGACAACATCCGGGAGATGCTGATGGCATGAAGGGCCCAG

Alignment

ORF - retro_mmur_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPVDLELKKXFTELQAKVIDTQ-KVKLADIQ-EQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFIL
          MAAPVDLELKK.FTELQAKVIDTQ.KVKLADIQ.EQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFIL
Retrocopy MAAPVDLELKKAFTELQAKVIDTQQKVKLADIQIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFIL

Parental  QSKEVIHNQLLEKQRIAEDKIKELEQKKSYLERSVKEAEDNIREMLMARRAQ
          QSKEVIHNQLLEKQRIAEDKIKELEQKKSYLERSVKEAEDNIREMLMA.RAQ
Retrocopy QSKEVIHNQLLEKQRIAEDKIKELEQKKSYLERSVKEAEDNIREMLMA*RAQ

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_1121 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1121 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 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Felis catus	ENSFCAG00000001272	1 retrocopy	retro_fcat_1323,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Microcebus murinus	ENSMICG00000000349	1 retrocopy	retro_mmur_1121 ,
Oryctolagus cuniculus	ENSOCUG00000009432	4 retrocopies	retro_ocun_1049, retro_ocun_1885, retro_ocun_804, retro_ocun_999,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Rattus norvegicus	ENSRNOG00000018653	1 retrocopy	retro_rnor_985,