RetrogeneDB ID: retro_tsyr_2124

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_9330:26395..27402(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSTSYG00000005482
• Aliases: None
• Description: family with sequence similarity 20, member B [Source:HGNC Symbol;Acc:23017]

Sequence

>retro_tsyr_2124
CGAGAGGTGTACCCTGAAGAGACACCAGAGCTGGGAGCAATCGTGCATGCCACGACCACCAAGAAAATCATTAGAGCTGA
TGTGGGTTATAAAGGGACACAGCTGAAAGCCTTACTAATACTTGAAGGAGGACAGAAAATTGTCTTCAAGCCTAAGTGGT
ATAGCGGAAACTAATGATAGAAGGGGAGTCGTATGCCAGTTGCTATAGACACAATGCAGAGGTGGCAGCCTTTCACTTGG
ACAGAATTCTGGGTTTCCGCCAAGCCTCCTTGGTGGTTGGCAGATTTGTTAATCTTCAGACAGAGATCATATCTGTTGCC
ATGGAGCAGATGTTGAGCACATTCCTAACTGTTGGAAACAATACTTGTTTCTATGGGAAGTGTTATTACTGCCGAGAAAC
AGAGCCAGCATGTGCTGATGGAGACACAATAGACTTAGAGGGTTCTGTCACACTTTGGCTTCCAGACGTGTGGCCTCTGC
AGAAACACCAACATCTGTGAGGCAGGACTTACCAGGATGGCAAACTGGTCAGGTGGGAGTATGATGAGAGATACTGTGAT
GCAGTGAAGAAGACGTCCCCTTATGACTCTGGCCCATGCCTCTGGTACATCATTGACACAGTTGTCTTTGACTACCTGAT
TGACAATGCTGACCGCCATCACTATGAGAGCTTTCGAGACGAGGAGGGTGCTAGTATGCTTATCCTTCTCGATAATGCCA
AAAGCTTTGGGAACCCCTCGCTATATGAAAGAAGTATTCTTGCTCCCCTCTACCAGTGTTGCATCATTCGAGTTTCTACC
TGGCACATACTGAACTACCTGAAGAATGGTGTGCTAAAGTCTGCCTTAAAATCTACCATGGCCCATGACCTTATTTCCCC
AGTGCTCACCAATCCTCATTTGGACACCATGGACCAGCCGCTCCTGAGTGTCCTGGCCACGGTGAAGTAGTGCACTGACC
AGATTGGGATGGACACTGTACTGTTGGAAGACAGGATGCCTCTCTCC

Alignment

ORF - retro_tsyr_2124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.38 %
• Parental protein coverage: 81.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  REVYPEETPELGAIMHAMATKKIIKADVGYKGTQLKALLILEGGQKVVFKPKRYS-RDYVVEGEPYAGYD
          REVYPEETPELGAI.HA..TKKII.ADVGYKGTQLKALLILEGGQK.VFKPK.YS.R....EGE.YA...
Retrocopy REVYPEETPELGAIVHATTTKKIIRADVGYKGTQLKALLILEGGQKIVFKPKWYS<RKLMIEGESYASCY

Parental  RHNAEVAAFHLDRILGFRRAPLVVGRFVNLRTEIKPVATEQLLSTFLTVGNNTCFYGKCYYCRETEPACA
          RHNAEVAAFHLDRILGFR.A.LVVGRFVNL.TEI..VA.EQ.LSTFLTVGNNTCFYGKCYYCRETEPACA
Retrocopy RHNAEVAAFHLDRILGFRQASLVVGRFVNLQTEIISVAMEQMLSTFLTVGNNTCFYGKCYYCRETEPACA

Parental  DGDT--MEGSVTLWLPDVWPLQKHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTAV
          DGDT...EGSVTLWLPDVWPLQKH.H..GRTY..GKL.RWEYDE.YCDAVKKTSPYDSGP.L..IIDT.V
Retrocopy DGDTIDLEGSVTLWLPDVWPLQKHQHL*GRTYQDGKLVRWEYDERYCDAVKKTSPYDSGPCLWYIIDTVV

Parental  FDYLIGNADRHHYESFQDDESTTF-ILLDNAKSFGNPSLDERSILAPLYQCCIIRVSTWNRLNYLKNGVL
          FDYLI.NADRHHYESF.D.E.....ILLDNAKSFGNPSL.ERSILAPLYQCCIIRVSTW..LNYLKNGVL
Retrocopy FDYLIDNADRHHYESFRDEEGASMLILLDNAKSFGNPSLYERSILAPLYQCCIIRVSTWHILNYLKNGVL

Parental  KSALKSAMAHDPISPVLSDPHLDTMDQRLLSILATVKQCTDQFGMDTVLVEDRMPLS
          KSALKS.MAHD.ISPVL..PHLDTMDQ.LLS.LATVK.CTDQ.GMDTVL.EDRMPLS
Retrocopy KSALKSTMAHDLISPVLTNPHLDTMDQPLLSVLATVK*CTDQIGMDTVLLEDRMPLS

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_2124 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 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484, retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124 , retro_tsyr_89,