RetrogeneDB ID: retro_mmur_671

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_4577:655167..657203(-)
• Located in intron of: ENSMICG00000003442

Retrocopy information

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

Parental gene information

• Parental gene symbol: THRAP3
• Ensembl ID: ENSMICG00000007920
• Aliases: None
• Description: thyroid hormone receptor associated protein 3 [Source:HGNC Symbol;Acc:22964]

Sequence

>retro_mmur_671
ATGTCAAAAACAAACAAATCCAAGTCTGGATCTCGCTCTTCTCGCTCAAGATCTGCATCAAGATCTCGTTCTCGTTCATT
TTCCAAGTCTCGGTCCCGAAGCCGATCTGTCTCTCGTTCAAGGAAGCGAAGGCTGAGTTCTAGGTCTCGGTCCAGATCAT
ATTCTCCAGCTCATAACAGAGAAGGAAATCACCCAAGAGTATATCAGAATCGGGATTTCAGAGGTCACAACAGAGGCTAT
AGAAGGCCCTATTATTTCCGTGGGCGCAACAGAGGCTTTTATCCATGGGGCCAATATAACCGAGGAGGCTATGGAAATTA
CCGCTCAAATTGGCAGAATTACCGGCAAGCATACAGTCCTCGGCGGGGTCGTTCGAGATCACGGTCCCCAAAGAGAAGAT
CTCCATCACCAAGGTCCAGGAGCCATTCTAGAAACTCCGATAAGTCTTCTTCTGATAGGTCAAGGCGTTCCTCATCCTCT
CGTTCTTCCTCTAACCACAGTCGAGTTGAATCTTCTAAGCGCAAGTCTGCAAAGGAGAAAAAGTCCTCTTCGAAGGATAG
CCGGCCATCTCAGGCTGCTGGGGATAACCAGGGAGATGAGGCCAAGGAGCAGACATTCTCTGGAGGAACCTCTCAAGATA
CAAAAGCATCTGAGAGTTCGAAGCCATGGCCAGATGCCACCACCTACAGTGCCGGCTCTGCATCACGGGGCTCAGCAGTA
TCTGATCTGAGTCCTCGGGAGCGAAGTCCAGCTCTCAAAAGCCCCCTCCAGTCTGTGGTGGTGAGGCGGCGGTCACCCCG
TCCTAGCCCTGTGCCAAAACCTAGTCCTCCACTTTCCAACACATCGCAGATGGGCTCAACTCTGCCGAGTGGTGGGTATC
AGTCTGGGACACACCAGGGTCAGTTTGACCATGGTTCTGGGTCCTTGAGTCCATCCAAAAAGAGCCCTGTGGGTAAGAGT
CCACCAGCCACTGGCTCCACATACGGCTCATCTCAGAAGGAGGAGAATGCTGCTTCAGGAGGAGCAGCCTATACAAAGAG
GTTCTGGAAGAGCAGAAGACAGAGAATGGAAAAGATAAGGAACAGAAACAAACAAATACTGATAAAGAGAAAATGAAAGA
GAAAGAGAGCTTCTCTGATACAGGCTTGAGTGATGCAAAGATGAAATCCGACCCATTTGCTCCCAAAGCTGATTCTGAGA
AGCCTTTTCGAGGCAGTCAGTCTCCCAAAAGATATAAGCTCCGAGATGACTTTGAGAAGAAGATGTCTGACTTCCACAAG
GAGGAGATGGATGATCAAGATAAAGACAAAGCTAAAGGAAGGAAGGAGTCTGAGTTTGATGATGAACCCAAATTTATGTC
TAAAGTTATAGCAGGTGCAAACAAAAATCAGGATGAGGAGAAGTCAGGCAAATGGGAGGGCCTGGTGTATGCACCTTCAG
GGAAGGAGAAGCAAAGGAAAACAGAGGAGCTGGAGGAGGAGTCTTTCGGAGAGAGATCCAAAAAGGAGGATCGGGGAGGG
ACCAAGAGAACCGAAAGTGGGCACAGGGGGTTTGTGCCCGAAAAGAATTTCCGAGTAACTGCTTACAAAGCAGTCCAGGA
GAAAAGCTCATCACCTCCCTCGAGAAAGACCTCTGAGAGCCAAGACAAGCTGGGAGCCAAAGGAGACTTTTCCTCAGGGA
AGTCTTCCTTTTCCATTACTCGAGAGGCCCAGGTCAATGTCCGGATGGACTCTTTTGATGAGGACCTTGCACAACCCAGT
GGCTTATTGGCTCAGGAACGCAAACTTTGTCGGGATCTAGTCCATAGCAACAAAAAGGAACAGGAATTTCGTTCCATTTT
CCAGCACATACAGTCAGCTCAGTCTCAGCGTAGCCCCTCAGAACTGTTTGCTCAGCATATAGTGACCATTGTTCATCACG
TTAAAGAGCATCACTTTGGGTCCTCAGGAATGACGTTGCATGAACGCTTTACTAAATACCTAAAGAGAGGAACTGAGCAG
GAGGCAGCTAAAAACAAGAAAAGCCCAGAGATACAC

Alignment

ORF - retro_mmur_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.38 %
• Parental protein coverage: 70.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKTNKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSVSRSRKRRLSSRSRSRSYSPAHNRERNHPRVYQN
          MSKTNKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSVSRSRKRRLSSRSRSRSYSPAHNRE.NHPRVYQN
Retrocopy MSKTNKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSVSRSRKRRLSSRSRSRSYSPAHNREGNHPRVYQN

Parental  RDFRGHNRGYRRPYYFRGRNRGFYPWGQYNRGGYGNYRSNWQNYRQAYSPRRGRSRSRSPKRRSPSPRSR
          RDFRGHNRGYRRPYYFRGRNRGFYPWGQYNRGGYGNYRSNWQNYRQAYSPRRGRSRSRSPKRRSPSPRSR
Retrocopy RDFRGHNRGYRRPYYFRGRNRGFYPWGQYNRGGYGNYRSNWQNYRQAYSPRRGRSRSRSPKRRSPSPRSR

Parental  SHSRNSDKSSSDRSRRSSSSRSSSNHSRVESSKRKSAKEKKSSSKDSRPSQAAGDNQGDEAKEQTFSGGT
          SHSRNSDKSSSDRSRRSSSSRSSSNHSRVESSKRKSAKEKKSSSKDSRPSQAAGDNQGDEAKEQTFSGGT
Retrocopy SHSRNSDKSSSDRSRRSSSSRSSSNHSRVESSKRKSAKEKKSSSKDSRPSQAAGDNQGDEAKEQTFSGGT

Parental  SQDTKASESSKPWPDATTYSAGSASRGSAVSDLSPRERSPALKSPLQSVVVRRRSPRPSPVPKPSPPLSN
          SQDTKASESSKPWPDATTYSAGSASRGSAVSDLSPRERSPALKSPLQSVVVRRRSPRPSPVPKPSPPLSN
Retrocopy SQDTKASESSKPWPDATTYSAGSASRGSAVSDLSPRERSPALKSPLQSVVVRRRSPRPSPVPKPSPPLSN

Parental  TSQMGSTLPSGGYQSGTHQGQFDHGSGSLSPSKKSPVGKSPPATGSTYGSSQKEENAASGGAAYTKRY-M
          TSQMGSTLPSGGYQSGTHQGQFDHGSGSLSPSKKSPVGKSPPATGSTYGSSQKEENAASGGAAYTKR...
Retrocopy TSQMGSTLPSGGYQSGTHQGQFDHGSGSLSPSKKSPVGKSPPATGSTYGSSQKEENAASGGAAYTKRF<L

Parental  EEQKTENGKDKEQKQTNTDKEKMKEKGSFSDTGLGDAKMKSDPFAPKADSEKPFRGSQSPKRYKLRDDFE
          EEQKTENGKDKEQKQTNTDKEKMKEK.SFSDTGL.DAKMKSDPFAPKADSEKPFRGSQSPKRYKLRDDFE
Retrocopy EEQKTENGKDKEQKQTNTDKEKMKEKESFSDTGLSDAKMKSDPFAPKADSEKPFRGSQSPKRYKLRDDFE

Parental  KKMSDFHKEEMDDQDKDKAKGRKESEFDDEPKFMSKVIAGANKNQDEEKSGKWEGLVYAPSGKEKQRKTE
          KKMSDFHKEEMDDQDKDKAKGRKESEFDDEPKFMSKVIAGANKNQDEEKSGKWEGLVYAPSGKEKQRKTE
Retrocopy KKMSDFHKEEMDDQDKDKAKGRKESEFDDEPKFMSKVIAGANKNQDEEKSGKWEGLVYAPSGKEKQRKTE

Parental  ELEEESFGERSKKEDRGGTKRTESGHRGFVPEKNFRVTAYKAVQEKSSSPPSRKTSESRDKLGAKGDFSS
          ELEEESFGERSKKEDRGGTKRTESGHRGFVPEKNFRVTAYKAVQEKSSSPPSRKTSES.DKLGAKGDFSS
Retrocopy ELEEESFGERSKKEDRGGTKRTESGHRGFVPEKNFRVTAYKAVQEKSSSPPSRKTSESQDKLGAKGDFSS

Parental  GKSSFSITREAQVNVRMDSFDEXXXXPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSEL
          GKSSFSITREAQVNVRMDSFDE....PSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSEL
Retrocopy GKSSFSITREAQVNVRMDSFDEDLAQPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSEL

Parental  FAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIH
          FAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIH
Retrocopy FAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIH

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_671 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_671 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
Canis familiaris	ENSCAFG00000003389	1 retrocopy	retro_cfam_549,
Microcebus murinus	ENSMICG00000007920	1 retrocopy	retro_mmur_671 ,
Mus musculus	ENSMUSG00000043962	1 retrocopy	retro_mmus_2939,
Pan troglodytes	ENSPTRG00000000535	1 retrocopy	retro_ptro_1771,
Rattus norvegicus	ENSRNOG00000009977	1 retrocopy	retro_rnor_674,