RetrogeneDB ID: retro_tsyr_1606

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_508943:545..815(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF4
• Ensembl ID: ENSTSYG00000011244
• Aliases: None
• Description: ring finger protein 4 [Source:HGNC Symbol;Acc:10067]

Sequence

>retro_tsyr_1606
GATGAGGAATGGTGCAGGGACAGAGATGAGTACGTAACTACCCATATTCCCAGAAACACCAGAGATAAGGAATCTACAGG
ACTGACTCAGGTCAGTTGCCCAATCACATGGACAGATACTCAGAAATTGTGCAGAACAGACGTCTCATTGTTTCTGCAGA
ATGTGGCCAGCATCTTCTGTAGCCAGTGCCTCTGGGATTCCCTCTAGTATGCTTACACTTGCACAGGAAGGAAAAAGATC
AACCTCAAATGGTACTACCCTATTTGTATA

Alignment

ORF - retro_tsyr_1606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.71 %
• Parental protein coverage: 64.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DEELSRDRDVYVTTHTPRNARDEGATGLRPLGTVSCPIC-MDGYSEIVQNGRLIVSTECGH-VFCSQCLR
          DEE..RDRD.YVTTH.PRN.RD...TGL.....VSCPI..MD.YSEIVQN.RLIVS.ECG...FCSQCL.
Retrocopy DEEWCRDRDEYVTTHIPRNTRDKESTGLT---QVSCPIT<MDRYSEIVQNRRLIVSAECGQ>IFCSQCLW

Parental  DSLKNANTCPTCRKKINHKRYHPIYI
          DSL..A.TC.T.RKKIN.K.Y.PI.I
Retrocopy DSL*YAYTC-TGRKKINLKWYYPICI

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_1606 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Homo sapiens	ENSG00000063978	1 retrocopy	retro_hsap_319,
Gorilla gorilla	ENSGGOG00000015149	2 retrocopies	retro_ggor_1144, retro_ggor_345,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Microcebus murinus	ENSMICG00000001767	1 retrocopy	retro_mmur_1265,
Mus musculus	ENSMUSG00000029110	1 retrocopy	retro_mmus_522,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Otolemur garnettii	ENSOGAG00000010776	1 retrocopy	retro_ogar_2121,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Pteropus vampyrus	ENSPVAG00000017017	1 retrocopy	retro_pvam_167,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,
Tarsius syrichta	ENSTSYG00000011244	1 retrocopy	retro_tsyr_1606 ,