RetrogeneDB ID: retro_tsyr_111

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_3031:29328..30013(-)
• Located in intron of: ENSTSYG00000003943

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOLR1
• Ensembl ID: ENSTSYG00000003503
• Aliases: None
• Description: folate receptor 1 (adult) [Source:HGNC Symbol;Acc:3791]

Sequence

>retro_tsyr_111
ATGGCACAGCAGATGGCAACACAGTTGCTGCTCCTTCTAGTGTGGGTGGCCGCTGTGGGGGGAACCCGATCCAGGACTCT
GCGGATCTGGACTGAACTTCTCAACATCTGCATGGACACCAAGTACCACAAGGAAAAACCAAACCCGGAGGACAAGCTGC
ATGAGCAGTGCCAGTCCCTGGAGGAAGAATGCCTGCTGCTCCACCAACACCAGCCTGGAAACCCACAAGGACATTTCCTA
CCTATACAGATTCAACTGGGACCACTGTGGAGAGATGGCACCTGCCTGCAAATGGCACTTTACCCAGGACACCGGCCTCT
ACAAGTGCTCCCCCAACTTGGGACCCTGGATCCAGCAGGTGGACCAAAGCTGGCGCAAAGAGCGGATCCTAAACATGCCC
CTGTGCAAGGAGGACTGTCAGCGCTGGCGGTAGGACTGTTGCATCTCCTACACCTGCAAGAGCAACTGGCACAAGGGCTG
GAACTGGACCTCAGGAAATAACAAGTGCCCAGTGGGAGCTGCCTGCCACCCTTTCCATTTCTACTTTCCCACACCTAGGG
CCCTGTGCAATGAAATCTGGAGCCACTCCTACAAAGACAGCAACTACAGCTGAGGGAGTGACCGCTGCATCCAGATGTGG
TTTGACCCTACCCAAGGCAACCCCAATGAGGAGGTGGCAAGGTTC

Alignment

ORF - retro_tsyr_111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.15 %
• Parental protein coverage: 88.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQRMETQLLLLLVWAAAVGGTRSRTPRTRTELLNVCMDAKHHKEKPSREDKLHEQC-SPWRKNACCSTN
          MAQ.M.TQLLLLLVW.AAVGGTRSRT.R..TELLN.CMD.K.HKEKP..EDKLHEQC.SPWRKNACCSTN
Retrocopy MAQQMATQLLLLLVWVAAVGGTRSRTLRIWTELLNICMDTKYHKEKPNPEDKLHEQC>SPWRKNACCSTN

Parental  TSLEAHKDISYLYRFNWDHCGEMAPACKRHFIQDTCLYECSPNLGPWIQQVNQSWRKERILNVPLCKEDC
          TSLE.HKDISYLYRFNWDHCGEMAPACK.HF.QDT.LY.CSPNLGPWIQQV.QSWRKERILN.PLCKEDC
Retrocopy TSLETHKDISYLYRFNWDHCGEMAPACKWHFTQDTGLYKCSPNLGPWIQQVDQSWRKERILNMPLCKEDC

Parental  QQWWEDCRTSYTCKSNWHKGWNWTSGNNECPVGSACYSFHFYFPTPEALCNEIWSHSYKVSNYSRGSGRC
          Q.W..DC..SYTCKSNWHKGWNWTSGNN.CPVG.AC..FHFYFPTP.ALCNEIWSHSYK.SNYS.GS.RC
Retrocopy QRWR*DCCISYTCKSNWHKGWNWTSGNNKCPVGAACHPFHFYFPTPRALCNEIWSHSYKDSNYS*GSDRC

Parental  IEMWFDPAQGNPNEEVARF
          I.MWFDP.QGNPNEEVARF
Retrocopy IQMWFDPTQGNPNEEVARF

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_111 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111 , retro_tsyr_1651,