RetrogeneDB ID: retro_ogar_2224

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873604.1:3100929..3101420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000026693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000003462
• Aliases: None
• Description: None

Sequence

>retro_ogar_2224
CTCTTTCCCTCCGGCCGCGCGGATACCCGTCGGTCGGGCGAGCAGCCGCAGCTCGGCCGCCCTGGGCTTCTTTGGTTGGT
CTGCAGCTGCTGGTGATGATGGCGCCGTCGCCGTGGAAGGGGCTAGTGGGCGCCGGCCTCTTCGCCCTGGCCCACGCCGC
CTTTTCCGCGGCTCAGCATCGCTCTTACATGCGATTAACAGAAAAGGAGGATGAGTCGCTGCCAGTGGATATCGTGCTTC
AGACGCTTCTGGCCTTTGCAGTTACCTGTTACGGTATAGTTCGTATTGCAGGGGAGTTTAAAGACGTGGATGCCACTTCA
GAACTAAAAAATAAGACATTTGATACAGTAAGGAATCGCCCATCCTTTTGTGTATTTAATCATCGTGGCCAAGTACTGCC
CCGGCCTTCGGATAAATCAGATTCTTCAAACCAAGACGCCTTGTCCTCTAACACATCATCGAAGTTACGCAAACTCGAAT
CACTGCGTCGT

Alignment

ORF - retro_ogar_2224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.21 %
• Parental protein coverage: 84.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFPR-RADTGRWKKEP-LRRPSLFLLVCSSF-GIMAPSLWKGLVGVGLFALAHAAFSAAQHRSYMRLTEK
          .FP..RADT.R....P.L.RP.L..LVCS.....MAPS.WKGLVG.GLFALAHAAFSAAQHRSYMRLTEK
Retrocopy LFPSGRADTRRSGEQPQLGRPGLLWLVCSCW<VMMAPSPWKGLVGAGLFALAHAAFSAAQHRSYMRLTEK

Parental  EDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDT
          EDESLP.DIVLQTLLAFAVTCYGIV.IAGEFKD.DATSELKNKTFDT.RN.PSF.VFNHRG.VL.RPSD.
Retrocopy EDESLPVDIVLQTLLAFAVTCYGIVRIAGEFKDVDATSELKNKTFDTVRNRPSFCVFNHRGQVLPRPSDK

Parental  SNSSNQDALSSNTSLKLRKLESLRR
          S.SSNQDALSSNTS.KLRKLESLRR
Retrocopy SDSSNQDALSSNTSSKLRKLESLRR

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_2224 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224 ,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,