RetrogeneDB ID: retro_pabe_3039

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6_random:9418559..9419744(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSPPYG00000000046
• Aliases: None
• Description: transcription factor B2, mitochondrial [Source:HGNC Symbol;Acc:18559]

Sequence

>retro_pabe_3039
ATGTGGATCCCAGTGGCCGGGCTTCCTCCTTGGCTGAGGCTCTCCGCCTTGGGGGGCGCTGGTCACTTTTGCATTTTAGG
GTCTGGAGCAGTGACGCAAAAGCACTTACCGGCGAGGAACCGCCGTGGCCTGTCTGACTCCTCTCCGCAGCTGTGGCCCG
ATCCAGATTTCAGGGACCCGCCAAGGAGGGTGTCTATGTCCAGCTTAGACTTTAAGCATTACATAACCAATCGGAGATTG
GCTGAGACCCTGGCGCAAATTGTATGGAGAAAACAAAATAGACCTCCACACCTATTGCTGCAGTGCAGTCCAGGTCCTGG
AATCCTGACTCAGGCATTACTTGAAGTTGGTGCCAAAGTGGTTGCCCTTGAAAGTGACAAAACTTTTATTCCACATTTGG
AGTCCTTAGGAAAAAATCTGGATGGAAAACTACAAGTGATTCACTGTGACTTCTTTAAAATAGATCCTAGAAGTGGTGGA
GTAATAAAACCACCCGCTATGGCTTCTCAAGGGCTCTTTCAGAATTTGGGAATAGAAGCAGTTCCTTGGACAGCAGGCAT
CCCTTTAAAAGTAACTGGAATGTTCTCAAGTAAGGGTGAAAAAAAAGGCCACTTTGGAAACCTGCATATGACGTATTCCT
GTACTTCTATATATAAATTTGGATGAATAGAATGAAATACGTTGATTGGTGAAAAAGAATTCCAGAAACTAACGCCAGAT
CCCCGAAATCCAGACTTGTATCATGTATGAAGTGTTATCTGGCAAGTAGCTTGTGAGATTAAGGTTCTGCACATGGAGCC
TTGCTCATCATTTGATGTACACACCCAAAATGGGAGGCTGGAAAACTCAAAGTGTAGGGAATTATTAGAACTATTACAAC
AAAATCTGTATCTTATTCGAATGGCTCCTCATAGAAATTTATTTACCGAGAACTTAACACCTATTAACTACAATATATTT
TTTCGCATGTTAAAGCACTGTTTTGGGGGGTGCAGTGCCAATCTAATAGACCACTTACGTTCATTGACTCCACTTGATGC
AATGGATATATTGATGCAAATAGGAAAAAAGGAAGAAGAGAAAATAACTAACATGTACCCTCACGACTTCAAAAACCTTT
TTGAAACTATAGAGTGTTCCAAAGATTGTGCTTATATATGGCTATATGATGAAACCCTGGAAGAT

Alignment

ORF - retro_pabe_3039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.72 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWIPVAGLPRRLRLSALAGAGRFCILGSEAATRKHLPARNSCGLSDSSPQLWPEPDFRHQPKKASKSSLD
          MWIPVAGLP..LRLSAL.GAG.FCILGS.A.T.KHLPARN..GLSDSSPQLWP.PDFR..P...S.SSLD
Retrocopy MWIPVAGLPPWLRLSALGGAGHFCILGSGAVTQKHLPARNRRGLSDSSPQLWPDPDFRDPPRRVSMSSLD

Parental  FKRYVTDRRLAETLAQIYLGKPNRPPHLLLECNPGPGILTQALLEAGAKVVALESDKTFIPHLESLGKNL
          FK.Y.T.RRLAETLAQI...K.NRPPHLLL.C.PGPGILTQALLE.GAKVVALESDKTFIPHLESLGKNL
Retrocopy FKHYITNRRLAETLAQIVWRKQNRPPHLLLQCSPGPGILTQALLEVGAKVVALESDKTFIPHLESLGKNL

Parental  DGKLRVIHCDFFKIDPRSGGVIKPPAMSSRGLFKNLGIEAVPWTADIPLKVVGMFPSRDEKRALWKLAYD
          DGKL.VIHCDFFKIDPRSGGVIKPPAM.S.GLF.NLGIEAVPWTA.IPLKV.GMF.S.............
Retrocopy DGKLQVIHCDFFKIDPRSGGVIKPPAMASQGLFQNLGIEAVPWTAGIPLKVTGMFSSKGXXXGHFGNLHM

Parental  LYSCTSIYKFGRIEVNMFIGEKEFQKLMADPRNPELYHVLSVIWQVACEIKVLHMEPSSSFVVYTRKGPL
          .YSCTSIYKFG.IE.N..IGEKEFQKL..DPRNP.LYHV.SVIWQVACEIKVLHMEP.SSF.V.T..G.L
Retrocopy TYSCTSIYKFG*IE*NTLIGEKEFQKLTPDPRNPDLYHV*SVIWQVACEIKVLHMEPCSSFDVHTQNGRL

Parental  ENPKRRELLDLLQQKLYLIQMTPRQNLFTKNLTPMNYNIFFHLLKHCFGRRSATVVDHLRSLTPLDARDI
          EN.K.RELL.LLQQ.LYLI.M.P..NLFT.NLTP.NYNIFF..LKHCFG..SA...DHLRSLTPLDA.DI
Retrocopy ENSKCRELLELLQQNLYLIRMAPHRNLFTENLTPINYNIFFRMLKHCFGGCSANLIDHLRSLTPLDAMDI

Parental  LMQIGKQEDQKVVNMYPQDFKTLFETIECSKNCAYRWLYDETLED
          LMQIGK.E..K..NMYP.DFK.LFETIECSK.CAY.WLYDETLED
Retrocopy LMQIGKKEEEKITNMYPHDFKNLFETIECSKDCAYIWLYDETLED

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.22 RPM	2.71 RPM
SRP007412_cerebellum	0.36 RPM	4.74 RPM
SRP007412_heart	0.00 RPM	2.38 RPM
SRP007412_kidney	0.07 RPM	5.14 RPM
SRP007412_liver	0.06 RPM	4.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3039 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3039 has 0 orthologous retrocopies within eutheria group .

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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,