RetrogeneDB ID: retro_ogar_2187

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873600.1:3118450..3119238(+)
• Located in intron of: ENSOGAG00000000385

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSOGAG00000007823
• Aliases: None
• Description: transcription factor B2, mitochondrial [Source:HGNC Symbol;Acc:18559]

Sequence

>retro_ogar_2187
CCAGATGTTGTCAGCGAGCATCAGGGGGTTGCTGGTCACTTTTGCCTTTTGGGGTCCGGAATGGCGACGCGAATGGACTT
GCCATTGGGGAACCATGGCAGCTTATCTTAGTCCTGTCTACAGGAGTTGCCCTATCCGGATTTCAACGAATCACCCTCTG
TGGTGTCCAAGTGCTGAGGACAACCAAAGTGCTATGTAAGCAATCAGAAATTAGCCAAGGCCGTGGCCCATATTCTGCAG
GGGAGACGAAGAACTCAACAACTATTACTGGAGTGCAATCCAGGTCCCGGAATCCTGACTCAGGCATTGCTTGAAACTGG
TTCCACAGTGGTTGCCCTTGAAATCGACAGAACATTTATTCCACATTTGGAGACCTCAGGAAACAATCTGGATGGACAGC
TAGATGTCCACTGTGACTTCTTTAAAATGGATCCTAGAAATAGCACACAAGTCAAACCACCCATTCTGCTTTCACATACG
CTTTTTCAGAATTTGGGAATAAAGGCACGTCCTTGGTCAGCAGGTATACCTTTAAAAGTAATTGGAATTTTCGCAATTAG
AAGTGAAAGAAAGGCACTTTGGAAACCCTTCTATGACCTCTATTCCTGTACTTTTGTATATAAATATGGATGAATAGAAC
TAAATATGTTTATTGGTGAAAAAGAATACCAGAGAGTAGTGGCTACTCCCAGCAACTCAAACTTGTATCAGGCGTGGAGT
GTGCTCTGGCAAGTAGCTTGTGAGATTAAGCTTCTGCAGTGGAGCCTTGGTCATCATTCGATATACAT

Alignment

ORF - retro_ogar_2187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 66.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRLMLSALGGAGRFCLLGSGTATRKDLPSRNCRGLSESCPQELPYPDFNESPSVVSKCRGEPKRYISSRK
          P.......G.AG.FCLLGSG.ATR.DLP..N...LS.SC.QELPYPDFNESPSVVSKC.G.PK.Y.S..K
Retrocopy PDVVSEHQGVAGHFCLLGSGMATRMDLPLGNHGSLS*SCLQELPYPDFNESPSVVSKC*GQPKCYVSNQK

Parental  LAETVAHILQRRRRTQQLLLECNPGPGILTQALLETGATVVALESERTFIPHLETLGNNLDGQLDVIHCD
          LA..VAHILQ.RRRTQQLLLECNPGPGILTQALLETG.TVVALE..RTFIPHLET.GNNLDGQLDV.HCD
Retrocopy LAKAVAHILQGRRRTQQLLLECNPGPGILTQALLETGSTVVALEIDRTFIPHLETSGNNLDGQLDV-HCD

Parental  FFKMDPRNSIQVKPPILLSHMLFPNLGIKARPWSAGIPLKVIGIFPFRSERKVLWKLLYDLYSCTSVYKY
          FFKMDPRNS.QVKPPILLSH.LF.NLGIKARPWSAGIPLKVIGIF..RSERK.LWK..YDLYSCT.VYKY
Retrocopy FFKMDPRNSTQVKPPILLSHTLFQNLGIKARPWSAGIPLKVIGIFAIRSERKALWKPFYDLYSCTFVYKY

Parental  GRIELNMFIGEKEYQRLVATPSDSNLYQAWSVLWQVACEIKLLH-TEPWSSFNIY
          G.IELNMFIGEKEYQR.VATPS.SNLYQAWSVLWQVACEIKLL...EPWSSF.I.
Retrocopy G*IELNMFIGEKEYQRVVATPSNSNLYQAWSVLWQVACEIKLLQ<VEPWSSFDIH

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_2187 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013225	1 retrocopy	retro_cpor_451,
Homo sapiens	ENSG00000162851	1 retrocopy	retro_hsap_3548,
Gorilla gorilla	ENSGGOG00000001095	1 retrocopy	retro_ggor_2396,
Myotis lucifugus	ENSMLUG00000003923	1 retrocopy	retro_mluc_1302,
Macaca mulatta	ENSMMUG00000022915	1 retrocopy	retro_mmul_1814,
Nomascus leucogenys	ENSNLEG00000004146	1 retrocopy	retro_nleu_2323,
Oryctolagus cuniculus	ENSOCUG00000013727	2 retrocopies	retro_ocun_1557, retro_ocun_236,
Otolemur garnettii	ENSOGAG00000007823	2 retrocopies	retro_ogar_1444, retro_ogar_2187 ,
Pongo abelii	ENSPPYG00000000046	1 retrocopy	retro_pabe_3039,
Pan troglodytes	ENSPTRG00000002188	1 retrocopy	retro_ptro_2412,