RetrogeneDB ID: retro_tsyr_615

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_151300:2988..3919(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIFM1
• Ensembl ID: ENSTSYG00000000060
• Aliases: None
• Description: apoptosis-inducing factor, mitochondrion-associated, 1 [Source:HGNC Symbol;Acc:8768]

Sequence

>retro_tsyr_615
CTTCAGAATATTACGATTATTGGTGGGGGCTTCCTCGGTAGTGAACTGGCCTGTTCTCTTGGCAGAAAGGCTCGAGCCAT
GGGCACAGAAGTGATTCAGCTCTTCCCTGAGAAAGGAAATATAGGAAAGATCCTCCCCGAATACCTCAGCAACTGAACCA
TGGAAAAAATCTGATGAGAAGGGGTTAAGGTGATGCCTAATGCTATTGTGCAATCAGTTGGAGTCAGCGGTAGCAAGTTA
TTCATCAAGTTGAAAGACTGCAGTAAGGTAGAAACGGACCACATAGTGGCAGCTGTGGGCCTAGAGGCTAATGCTGAGTT
GGTTAAGACTGGTGGGCTGGAGATAGACTCAGATTTTGGTGGCTTCTGGGTAAATGCAGAACTCCAAGCACACTCCAACA
TCTGGGGGGCAGGGATGCTGAGTGTTTCTATGATATAAAGTTGGGAAAGAGGCGAGTAGAACACCATGATCATGCTGTTG
TAAGCGGAAGATTGGCTGGGGAAAACTTGGAGTTGTGAAGTTGTACTGGCATCAGTCCATGTTCTGGAGCGATTTGGGCC
CTAATGTTGGCTATGAAGCTATTGGTCTTGTGGACAATAGTTTGCCCACAGTTGGTGTTTTTGCAAAAGCAACTGCACAA
GACTACCCAAAATCTGCACAGTCAGGGACTGGTATCTCATCAGAGAGTGAGACAGAGCCCAAGGTCTCAGAAATTACTAT
TCCTCCCAGCACTCCTGCAGTTCCAAAGGCTCCTGTCCAAGGGGAGGACTATGGTAAAGGCATCATTTTCTACCTCAGGG
ACAAAGTGGTCGTGGGGATTGTACTATGGAACATCTTTAACGAAATGCCAATAGCAAGGAAGATCATTAAGGATGGTGAG
CAACATGAAGATCTCAATGAAGTAGCCAAACTGTTCAAGATCCAGGAAGAC

Alignment

ORF - retro_tsyr_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.01 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKSITIIGGGFLGSELACALGRKAQALGTEVIQLFPEKGNMGKILPEYISNWTMEKVRREGVKVMPNAIV
          ...ITIIGGGFLGSELAC.LGRKA.A.GTEVIQLFPEKGN.GKILPEY.SN.TMEK...EGVKVMPNAIV
Retrocopy LQNITIIGGGFLGSELACSLGRKARAMGTEVIQLFPEKGNIGKILPEYLSN*TMEKI**EGVKVMPNAIV

Parental  QSVGVSGGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAG-D
          QSVGVSG.KL.IKLKD..KVETDHIVAAVGLE.N.EL.KTGGLEIDSDFGGF.VNAELQA.SNIW.AG.D
Retrocopy QSVGVSGSKLFIKLKDCSKVETDHIVAAVGLEANAELVKTGGLEIDSDFGGFWVNAELQAHSNIWGAG<D

Parental  AACFYDIKLGRRRVEHHDHAVVSG-RLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGV
          A.CFYDIKLG..R...H....V...R..G....G..K.YWHQSMFWSDLGP.VGYEAIGLVD.SLPTVGV
Retrocopy AECFYDIKLG-KRRVEHHDHAVVS<RKIGWGKLGVVKLYWHQSMFWSDLGPNVGYEAIGLVDNSLPTVGV

Parental  FAKATAQDNPKSATEQSGTGIRSESETESEASEIAIPPSTPAVPQAPVQGEDYGKGVIFYLRDKVVVGIV
          FAKATAQD.PKSA..QSGTGI.SESETE...SEI.IPPSTPAVP.APVQGEDYGKG.IFYLRDKVVVGIV
Retrocopy FAKATAQDYPKSA--QSGTGISSESETEPKVSEITIPPSTPAVPKAPVQGEDYGKGIIFYLRDKVVVGIV

Parental  LWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHED
          LWNIFN.MPIARKIIKDGEQHEDLNEVAKLF.I.ED
Retrocopy LWNIFNEMPIARKIIKDGEQHEDLNEVAKLFKIQED

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_615 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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
Dasypus novemcinctus	ENSDNOG00000018718	1 retrocopy	retro_dnov_767,
Homo sapiens	ENSG00000156709	1 retrocopy	retro_hsap_546,
Gorilla gorilla	ENSGGOG00000007635	1 retrocopy	retro_ggor_497,
Microcebus murinus	ENSMICG00000016006	1 retrocopy	retro_mmur_492,
Tarsius syrichta	ENSTSYG00000000060	1 retrocopy	retro_tsyr_615 ,