RetrogeneDB ID: retro_tsyr_1769

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_577911:57..444(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSTSYG00000003333
• Aliases: None
• Description: mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:14516]

Sequence

>retro_tsyr_1769
ATAGCAGCCTCTGTATTAAACACGCCGTTGAGGCGGCTTCCAGTCATCTCGTCCTTCCAAAGTGCCTACAGAGTTCAGGT
TCCCCTCCAGACTCTTTGCAGCAAAGCACCCCCTGAGAAAAATTCTTTGCCCCCAGTTCCCGTTTCACCTGATACGAATG
AGCCCTGGACACATTTGGAATCAGAAGACCAGGCCGTCTATGGTTCTCGCCCATCTGGGCTGACACCTGCCACCACCACA
AGGGTGGTATACCCCACAACGGACTCGAAAGACATGTATTCGTAAAAATAAAGTTGCCGGGAATCCCTGCCCCATCTGCA
GGGATCACAAGTTGCATGTCGACTTTAGAACGTGAAGCTCTTGGAACAGTTTGCGCTCACACGCACA

Alignment

ORF - retro_tsyr_1769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.12 %
• Parental protein coverage: 51.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASVLNTLLRRLPVISSFRSAYGVQVPLQALCNKASPEKDSLPLVPISPYKNEPWKYLESEEYQDRYGS
          .AASVLNT.LRRLPVISSF.SAY.VQVPLQ.LC.KA.PEK.SLP.VP.SP..NEPW..LESE..Q..YGS
Retrocopy IAASVLNTPLRRLPVISSFQSAYRVQVPLQTLCSKAPPEKNSLPPVPVSPDTNEPWTHLESED-QAVYGS

Parental  R-PVWADYRRNHKGGIP-PQRTRKTCIRKSKIAGNPCPICRDHKLHVDFR-NVKLLEQFVCAHT
          R.P.WAD....HKGGIP.PQRTRKTCIRK.K.AGNPCPICRDHKLHVDFR.NVKLLEQF....T
Retrocopy R<PIWADTCHHHKGGIP<PQRTRKTCIRKNKVAGNPCPICRDHKLHVDFR<NVKLLEQFALTRT

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_1769 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769 ,