RetrogeneDB ID: retro_tsyr_2096

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_89386:11493..12320(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1B2
• Ensembl ID: ENSTSYG00000010477
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2 [Source:HGNC Symbol;Acc:854]

Sequence

>retro_tsyr_2096
TATGCTGAGATTGTTCACTTGACATTACCAGACGGCACGAAGAGAAGTGGACAAGTTCTAGAAGTTAGTGGTTCCAAAGC
AGTGGTTCAGGTATTTGAAGGGACTTCAGGTATAGATGCTAAGAAAACGCCCTGTGAGTTTACTGGGGATATTCTCCGAA
TACCAGTGTCTGAAGACATGCTTGGTCGGGTAGTCAATGGATCAGGAAAACCCATCGACAGGGGTCCTGTTGTCCTGGTT
GAAGACTTCCTTGATCTCATGGGCCAGCCAATCAATCCTCAATGTCGAATCTACCCGGAGGAGATGATTCAGACTGGCAT
TTCGGCCACAGATGCATGAACATTATTGCTAGGGGACAGAAAATTCCTATCTTCTCTGCTGCTGAGTTACCACACAATGA
GATTGCAGCTCAAATCTGTTGCCAGGCTGGTTTGGTAAAGAAATCCAAAGATGTAGTGGACTACAGTGAGGAAAATTTTG
CAATTGTGCTTGCTGCTATGGCTGTAAACATGTAAACTGCCCAGTTCTTCAAATCTGACTTTGAAGAAAATGGCTCAATG
GACAATGTCTGTCTCTTTTTGAACTTGGCTAATGATCCAACTATTGAGTGAATTATCACTCCTCGCCTGGCTCTTACCAC
AGCTGAATTTCTGGCTTACCAGTGTGAGAAGCACGAACTGGTTATCCTAACAGACATGAGCTCTTATGCTGAAGCACTTC
GAGAGGTTTCCGCAGCCAGGGAAGAGGTTCCCGGTCAACGAGGCTTCCCAGGTTACATGTATACAGATTTAGCCACGATA
TATGAACGCACAGGTCAAGTGGAGGGT

Alignment

ORF - retro_tsyr_2096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 54.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGK
          YAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKT.CEFTGDILR.PVSEDMLGRV.NGSGK
Retrocopy YAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTPCEFTGDILRIPVSEDMLGRVVNGSGK

Parental  PIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDG-MNSIARGQKIPIFSAAGLPHNEIAAQI
          PIDRGPVVL.EDFLD.MGQPINPQCRIYPEEMIQTGISA.D..MN.IARGQKIPIFSAA.LPHNEIAAQI
Retrocopy PIDRGPVVLVEDFLDLMGQPINPQCRIYPEEMIQTGISATDA<MNIIARGQKIPIFSAAELPHNEIAAQI

Parental  CRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPR
          C.QAGLVKKSKDVVDYSEENFAIV.AAM.VNM.TA.FFKSDFEENGSMDNVCLFLNLANDPTIE.IITPR
Retrocopy CCQAGLVKKSKDVVDYSEENFAIVLAAMAVNM*TAQFFKSDFEENGSMDNVCLFLNLANDPTIE*IITPR

Parental  LALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEG
          LALTTAEFLAYQCEKH.LVILTDMSSYAEALREVSAAREEVPG.RGFPGYMYTDLATIYER.G.VEG
Retrocopy LALTTAEFLAYQCEKHELVILTDMSSYAEALREVSAAREEVPGQRGFPGYMYTDLATIYERTGQVEG

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_2096 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003668	1 retrocopy	retro_chof_2287,
Homo sapiens	ENSG00000147416	1 retrocopy	retro_hsap_4308,
Gorilla gorilla	ENSGGOG00000003888	1 retrocopy	retro_ggor_2879,
Microcebus murinus	ENSMICG00000001791	1 retrocopy	retro_mmur_854,
Nomascus leucogenys	ENSNLEG00000000794	1 retrocopy	retro_nleu_1460,
Pan troglodytes	ENSPTRG00000020040	1 retrocopy	retro_ptro_2917,
Tarsius syrichta	ENSTSYG00000010477	1 retrocopy	retro_tsyr_2096 ,
Tursiops truncatus	ENSTTRG00000013650	1 retrocopy	retro_ttru_1845,