RetrogeneDB ID: retro_ogar_3252

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873756.1:440888..441474(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000005901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CD164
• Ensembl ID: ENSOGAG00000015500
• Aliases: None
• Description: CD164 molecule, sialomucin [Source:HGNC Symbol;Acc:1632]

Sequence

>retro_ogar_3252
ATGTCGCTGCTCTCTTGCCGGCTGCTGTGGGCCACCACCTGCCTGGCCGCGCTCTGCAGTGCTATCTGCGGAACCGAACA
CGACCCTAGTCCCGCTCGGGACGACTGTGGAGACCACCACCAAGATAAACACGACCCTGGTGACAACCCCCGCACTGGTC
ACCACTCCGGTACCAGAAACCTGTGAAGGCCGAAACAGCTGTGCTTTCTGTACTAATACTAGCAATGTTAATACTACCTG
CTTTTGGATGGAATGTAAAGATAAGAGCTATTGGTCACATAATTCAACAGTTAGTGATTGTCAAGTGGTGAATGCAACAC
ACTTTTGTTCTGCTCCTACTACCATTCCAGCACCAACTAATTCTACAGCTGAAAACGCAACTCTGCCTTCTTCCTCTACA
ACTTCCACAGTTCCTACATCAGGTCCAACAAATACCACTTTGACTCCAACCTCACAACCTATTCGGAAATCTACCTTTGA
TGCAGCCAGTTTCATTGGCGGAATTGTCCTTGTCTTGGGCGTGCAGGCTGTAATTTTCTTTCTGTATAAATTCTGCAAAT
CTAAGGAACGAAATTACCACACTCTG

Alignment

ORF - retro_ogar_3252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSALSCRLLWATTCLAALCA-LSAEPNTTLAPLGTTVETTTKINTSLVTTPAPVTTPVPETCEGRNSCAS
          MS.LSCRLLWATTCLAALC..LSAEPNTTL.PLGTTVETTTKINT.LVTTPA.VTTPVPETCEGRNSCA.
Retrocopy MSLLSCRLLWATTCLAALCS>LSAEPNTTLVPLGTTVETTTKINTTLVTTPALVTTPVPETCEGRNSCAF

Parental  CTNTSNVNTTCFWMECKVIDKSYCSHNSTVSDCQVVNATHFCSVAPTTIPAPTNSTAENTTLPSSSTTST
          CTNTSNVNTTCFWMECK..DKSY.SHNSTVSDCQVVNATHFCS.APTTIPAPTNSTAEN.TLPSSSTTST
Retrocopy CTNTSNVNTTCFWMECK--DKSYWSHNSTVSDCQVVNATHFCS-APTTIPAPTNSTAENATLPSSSTTST

Parental  VPTSAGPTNTTLTPTSQPIRKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKSKERNYHTL
          VPTS.GPTNTTLTPTSQPIRKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKSKERNYHTL
Retrocopy VPTS-GPTNTTLTPTSQPIRKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKSKERNYHTL

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_3252 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017992	3 retrocopies	retro_btau_477, retro_btau_479, retro_btau_503,
Macaca mulatta	ENSMMUG00000007011	1 retrocopy	retro_mmul_2418,
Otolemur garnettii	ENSOGAG00000015500	2 retrocopies	retro_ogar_2245, retro_ogar_3252 ,
Tursiops truncatus	ENSTTRG00000004181	2 retrocopies	retro_ttru_436, retro_ttru_532,