RetrogeneDB ID: retro_tsyr_149

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_3902:52135..52622(-)
• Located in intron of: ENSTSYG00000010835

Retrocopy information

• Ensembl ID: ENSTSYG00000010867
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM96B
• Ensembl ID: ENSTSYG00000005006
• Aliases: None
• Description: family with sequence similarity 96, member B [Source:HGNC Symbol;Acc:24261]

Sequence

>retro_tsyr_149
GGGGCTGGCGGCGGCAGGGTAGGGGCGGCCTCTTGGAGAATGCCAACCCACTCATCTACGAGCGCTCTGGAGAGCGGCCA
TGACCGCCGGCAAGGACGAGCAGGTTCCCGACAGCATCGACGCACGCAAGATCTTCGATCTTATTTCCTCTATCAATGAC
CCAGAGCATCCTCTGACGCTAGAGCAGTTGAATGTACTAGAGCAAGTCCGGGTTCAGGTTAGCGACCCGGAGAGCACAGT
GACTGTGGCTTTCACACCCACCATTCCGCACTGCAGCATGGCCACCCTTATTGGCCTATCCATCAAGGTCAAGCTTCTTT
GCTCCCTTCCCCAGTGTTTCAAGATGGACGTGCACATTACACCTGGGACCCATGCCTCAGAGCATGCAGTGAACAAGCAG
CTTGCAGATAAGGAGCGGGTGGCAGCTGCCCTGGAGAACACCCACCTACTGGAGGTTGTGAATCAGTGCCTGTCAACCCG
CTCCCGA

Alignment

ORF - retro_tsyr_149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.57 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGGGGGVG-GGLLENANPLIYERSGERP-VTAGEEDEQVPDSIDAREIFDLIRSINDPEHPLTLEELNVV
          G.GGG.VG.GGLLENANPLIYERSGERP..TAG..DEQVPDSIDAR.IFDLI.SINDPEHPLTLE.LNV.
Retrocopy GAGGGRVG<GGLLENANPLIYERSGERP<MTAGK-DEQVPDSIDARKIFDLISSINDPEHPLTLEQLNVL

Parental  EQVRVQVSDPESTVAVAFTPTIPHCSMATLIGLSIKVKLLRSLPQRFKMDVHITPGTHASEHAVNKQLAD
          EQVRVQVSDPESTV.VAFTPTIPHCSMATLIGLSIKVKLL.SLPQ.FKMDVHITPGTHASEHAVNKQLAD
Retrocopy EQVRVQVSDPESTVTVAFTPTIPHCSMATLIGLSIKVKLLCSLPQCFKMDVHITPGTHASEHAVNKQLAD

Parental  KERVAAALENTHLLEVVNQCLSTRSR
          KERVAAALENTHLLEVVNQCLSTRSR
Retrocopy KERVAAALENTHLLEVVNQCLSTRSR

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_149 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609,
Canis familiaris	ENSCAFG00000020394	2 retrocopies	retro_cfam_479, retro_cfam_802,
Felis catus	ENSFCAG00000029216	2 retrocopies	retro_fcat_1464, retro_fcat_697,
Mustela putorius furo	ENSMPUG00000005303	2 retrocopies	retro_mputfur_1547, retro_mputfur_302,
Mus musculus	ENSMUSG00000031879	1 retrocopy	retro_mmus_2927,
Sarcophilus harrisii	ENSSHAG00000004698	1 retrocopy	retro_shar_590,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,
Tarsius syrichta	ENSTSYG00000005006	2 retrocopies	retro_tsyr_1305, retro_tsyr_149 ,