RetrogeneDB ID: retro_tsyr_1932

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_68831:8440..9041(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPF2
• Ensembl ID: ENSTSYG00000000038
• Aliases: None
• Description: D4, zinc and double PHD fingers family 2 [Source:HGNC Symbol;Acc:9964]

Sequence

>retro_tsyr_1932
CTTGGGAAGCAGCACTCCGAGGATGCCATGGAGCGCTGCCACCATGACAGTGCCCGTCTCTGTGCTGAGAGCAGTGTGCG
CCTGCCTTTCTTGGACTCCCAGGTCGGAGCAGCCCAGAGCAACCGTTACACCTGGATGGAAAAGAGACACCGGGGTCCAG
CACTGGCTTCTGGACAGCTGGGCTCCCACCCTGCCCAGCGCTGGCGGGAAAAGCGGCGAGCCCACCCCCCTGGGGATCCA
CGACTTTCCTCCCCATCTCTTAAACCAGACACAGACAAGACCCTGAAGAAGGAGGGGCTGATCTCTCCGGATGCAGTCGT
TGAGGGACCCTTGTGCGCACTGACCCCCTGGAGAAGCCAGGACCCCCAGACCCCCAGGGCTGATGATGACAGCCTGGGCG
AGCTTCCTGGGACCCACAGTTGAGCCCGGGAGCGCATCTTAGAACCAGATGACTTCCTGGATGACAGCGATGATGAGGAC
TAGGAAGGAGACACTCCCAAGCGTCCCGGCCAGGGGGAACTCAAGGGAAGGGGGTGGCAGTGCCCGCAAGAAGCTGGGCG
CTTCCCTCCTGGAGGTTCGGGACAAGCCCTGTGCCTATGAC

Alignment

ORF - retro_tsyr_1932 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LGEQYYKDAMEQCHNYNARLCAERSVRLPFLDSQTGVAQSNCYIWMEKRHRGPGLASGQLYSYPARRWRK
          LG.Q...DAME.CH...ARLCAE.SVRLPFLDSQ.G.AQSN.Y.WMEKRHRGP.LASGQL.S.PA.RWR.
Retrocopy LGKQHSEDAMERCHHDSARLCAESSVRLPFLDSQVGAAQSNRYTWMEKRHRGPALASGQLGSHPAQRWRE

Parental  KRRAHPPEDPRLSFPSIKPDTEQTLKKEGLISQDG-SSLEALLRTDPLEKRGAPDP-RVDDDSLGEFPVT
          KRRAHPP.DPRLS.PS.KPDT..TLKKEGLIS.D..S....L.RTDPLEK.G.PDP.R.DDDSLGE.P.T
Retrocopy KRRAHPPGDPRLSSPSLKPDTDKTLKKEGLISPDA<SR*GTLVRTDPLEKPGPPDP>RADDDSLGELPGT

Parental  NSRARKRILEPDDFLDDLDDEDYEEDTPKRRGKGKSKG-KGV-GSARKKLDASILEDRDKPYACD
          .S.AR.RILEPDDFLDD.DDED.E.DTPKR.G.G..KG.KGV.GSARKKL.AS.LE.RDKP.A.D
Retrocopy HS*ARERILEPDDFLDDSDDED*EGDTPKRPGQGELKG<KGV<GSARKKLGASLLEVRDKPCAYD

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_1932 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
Felis catus	ENSFCAG00000023858	1 retrocopy	retro_fcat_1341,
Homo sapiens	ENSG00000133884	1 retrocopy	retro_hsap_3660,
Macaca mulatta	ENSMMUG00000012317	1 retrocopy	retro_mmul_1794,
Nomascus leucogenys	ENSNLEG00000005574	1 retrocopy	retro_nleu_516,
Tarsius syrichta	ENSTSYG00000000038	1 retrocopy	retro_tsyr_1932 ,