RetrogeneDB ID: retro_ogar_1444

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873547.1:5437215..5438398(-)
• Located in intron of: None

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_1444
TTATGGGTTCCAATGGTGGGGCTTCCTCCTCTGCTGATGCTGTCAGCCTTGGGAAGTGCTGGTTGCTTTTGCTTTTTGGG
GTCCAGAACGGCAACACGAAAGGACTTGCCATTAGGGAACCGTTGTGGCTTGTCTGAGTCCTGCCCACAGGAGTTGCCTT
ATCCGGATTTCAACGAATCGCCCTCTGTGGTGTCCAAGTTCTGAGGAGAGCCCAAGCACTATGTAACCAGTCAGAAATTG
GCCGAGACCATGGCCCATATCTTACAGGGAAAAGGAAGAACTCACCAACTATTATTGGAGTGCAATCCAGGTCCTGGAAT
CCTGACTCAGGTATTGCTTGAAACTGGTGCCACAGTGGTTACCCTTGAAAGCATGAGAACATTTATTCCACATTTGGAGA
CCTTAGGAAAAAATCTGGATGGACAGCTAGAAGTCGTCCACTATGACTTCTTTAAAATGGATCCTAGAAATAGTATATAA
GTCAAACCACCCATTCTGCTTTCATGGACGCTTTTTCAGAATTTGGGAACAAAAGCATGTCCTTGGTCAGCAGGTGTACC
TTAAAAGTAATTGGAATTTTTCCAATTAGAAGTAAAAGAAAGGTACTTTGGAAAGTTTTATATAACCTATACTCCTGTAC
TTCTATATATAAATATGGACAAATAGAACTAAATATGTTTTATTGGTGAAAAAGAATACCAGAGACTAGTGGCTACTCCC
AGCAACTCAAACTTGTATCAACATGGAGGTCTCTGGCAAGTAGCTTGTGAGATTAAGCTTCTGCACGCAGAGCCTTGATC
ATCATTCGAGATATATAACCGAAATGGGGAACTGCGAAAGCCAAAGTGTAAGGGATAATTAGATCTAGCACAACAAAACC
TGTATGTTATTCAAATGCCTCCTCATAAGAATTTATTTACAGAAAACTTAATGCCTATTAACTATGATGTATTTTTTCAC
GTGTTAAAGCACTGTTTGGGGAAGCACAGTGCCAGGCTAATAGACCACTTACTCTTTGACTCCAGTTGATACAAGGCATA
TATTGAAAAAAATATGTAGAAATGAAAATGTGAAAGTAACTAATATATATCCTGAAGACTTTCAAAGCATTTTTGAAGCT
ATAGAGTGTTCCCAAGATCATGCTTATAAATGGCTATATGATGACAGCATGGAAGACACAAAG

Alignment

ORF - retro_ogar_1444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.5 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MWVPVVGLPPRLMLSALGGAGRFCLLGSGTATRKDLPSRNCRGLSESCPQELPYPDFNESPSVVSKCRGE
          .WVP.VGLPP.LMLSALG.AG.FC.LGS.TATRKDLP..N..GLSESCPQELPYPDFNESPSVVSK..GE
Retrocopy LWVPMVGLPPLLMLSALGSAGCFCFLGSRTATRKDLPLGNRCGLSESCPQELPYPDFNESPSVVSKF*GE

Parental  PKRYISSRKLAETVAHILQRRRRTQQLLLECNPGPGILTQALLETGATVVALESERTFIPHLETLGNNLD
          PK.Y..S.KLAET.AHILQ...RT.QLLLECNPGPGILTQ.LLETGATVV.LES.RTFIPHLETLG.NLD
Retrocopy PKHYVTSQKLAETMAHILQGKGRTHQLLLECNPGPGILTQVLLETGATVVTLESMRTFIPHLETLGKNLD

Parental  GQLDVIHCDFFKMDPRNSIQVKPPILLSHMLFPNLGIKARPWSAGIP-LKVIGIFPFRSERKVLWKLLYD
          GQL.V.H.DFFKMDPRNSI.VKPPILLS..LF.NLG.KA.PWSAG.P.LKVIGIFP.RS.RKVLWK.LY.
Retrocopy GQLEVVHYDFFKMDPRNSI*VKPPILLSWTLFQNLGTKACPWSAGVP<LKVIGIFPIRSKRKVLWKVLYN

Parental  LYSCTSVYKYGRIELNMF-IGEKEYQRLVATPSDSNLYQAWSVLWQVACEIKLLHTEPWSSFNIYNSNGE
          LYSCTS.YKYG.IELNMF.IGEKEYQRLVATPS.SNLYQ....LWQVACEIKLLH.EP.SSF.IYN.NGE
Retrocopy LYSCTSIYKYGQIELNMF>IGEKEYQRLVATPSNSNLYQHGG-LWQVACEIKLLHAEP*SSFEIYNRNGE

Parental  LRKLKRKESLD--QQNLYLIQMTPRKNLFTENLTPVNYDVFFHML-KHCFGKRSARLIDHL-HSLTPIDT
          LRK.K.K..LD..QQNLY.IQM.P.KNLFTENL.P.NYDVFFH.L.K..FG.........L..SLTP.DT
Retrocopy LRKPKCKG*LDLAQQNLYVIQMPPHKNLFTENLMPINYDVFFHVL<KALFGEAQCQANRPL<YSLTPVDT

Parental  RHILKKICINEKVKVTNIYPEEFKRIFEAIECSKDHAYKWLYDDSMEDTK
          RHILKKIC.NE.VKVTNIYPE.F..IFEAIECS.DHAYKWLYDDSMEDTK
Retrocopy RHILKKICRNENVKVTNIYPEDFQSIFEAIECSQDHAYKWLYDDSMEDTK

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_1444 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 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,