RetrogeneDB ID: retro_ogar_3169

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873734.1:481247..481955(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSOGAG00000008390
• Aliases: None
• Description: pentatricopeptide repeat domain 2 [Source:HGNC Symbol;Acc:25734]

Sequence

>retro_ogar_3169
CTCATCAAAGACCAGTGTCCACCAGGTTTTTCTCAGATATGACATCATACAATATTTTGATGGATATGTTATTATCAAGA
GTAAATATGAAAGTGCTTCAGAAGTATTGGTGGAGATGAAAAACTAAGATGTGAAGTTCATCAAAGATACCTATGTCCTT
GCTTGTGGAATTTTCTACAAACTGAATATCTCTGAATCTCTCAAAATCTGTACTATGTTTAGAGAAGAATCCCTAATCAA
AGGAGAAGCTCTCTCCAGGGAAGCATACTGTTTTGCTGTGACATCAGTTCTGAATCATAACCAGTGGAAAAAACTATGTC
CATTTTCTCTCAAATCATGGATCCAGAAAGCATAGCCTGCACTGATTTAAATATTATATTCCATATCCAGTCAAATATGT
TGGAAACCCCCATAAAGATACTAACAGATGCTGCAGAAGGAAATGTATGAAGATTTGTGAAAAGACATGTGTTCTCAGAA
GAAGTGCTGGCCAAAGTGAGGGAAAAAGTGAAGGGTGTGCCTGCCTTTTTGGCCAAATTTGATGAGATCTATGGGAAACT
GCACATCACTGGCCATGTCACCACTTGGACTTTAGATGACTTGCTCTGCTATACCCTCAGGGATAAGAAATCCCCCATGT
TGTCACTGAAGAAGAATACAGTCAGCCAGAGGACCCTCCAGCCACTCAGCAAGCCCCTGCTGGCTGAG

Alignment

ORF - retro_ogar_3169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIKDQSLRGF-FSDSTSYNILMDMLF-MKGEYESASEVLIEMKNQDVKFSKDTYVLAFAIFYKLNSPESL
          LIKDQ...GF.FSD.TSYNILMDML...K..YESASEVL.EMKN.DVKF.KDTYVLA..IFYKLN..ESL
Retrocopy LIKDQCPPGF<FSDMTSYNILMDMLL<IKSKYESASEVLVEMKN*DVKFIKDTYVLACGIFYKLNISESL

Parental  KMCTMLREEALIKGDVLSRRASCFAVALALNQNQ-VEKATSFYSQIMNPESIACANLKIIIHIQSNMLET
          K.CTM.REE.LIKG..LSR.A.CFAV...LN.NQ.VEK..S..SQIM.PESIAC..L.II.HIQSNMLET
Retrocopy KICTMFREESLIKGEALSREAYCFAVTSVLNHNQ<VEKTMSIFSQIMDPESIACTDLNIIFHIQSNMLET

Parental  LIKELADAAEGNVSRFVKRHVFSEEVLAKVREKVKAIPALLDRFDEIYGKLHITGHVTTQTLDDLLCHIP
          .IK.L.DAAEGNV.RFVKRHVFSEEVLAKVREKVK..PA.L..FDEIYGKLHITGHVTT.TLDDLLC...
Retrocopy PIKILTDAAEGNV*RFVKRHVFSEEVLAKVREKVKGVPAFLAKFDEIYGKLHITGHVTTWTLDDLLCYTL

Parental  KDKKSPMLFLNKRRISRRTLQPLNKSLLAE
          .DKKSPML.L.K...S.RTLQPL.K.LLAE
Retrocopy RDKKSPMLSLKKNTVSQRTLQPLSKPLLAE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3169 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169 ,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,