RetrogeneDB ID: retro_ptro_2412

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:5081795..5082739(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSPTRG00000002188
• Aliases: None
• Description: None

Sequence

>retro_ptro_2412
TTAGACTTTAAGCGTTACGTAACCAATCGGAGATTGGCTGAGACCCTGGCGCAAATCGTATGGAGAAAACAAAATAGACC
TCCACACCTATTGCTGCAGTGCAGTCCAGGTCCTGGAATCCTGACTCAGGCATTACTTGAAGTTGGTGCCAAAGTGGTTG
CCCTTGAAAGTGACAAAACTTTTATTCCACATTTGGAGTCCTTAGGAAAAAATCTGGATGGAAAACTACAAGTGATTCAC
TGTGACTTCTTTAAAATAGATCCTAGAAGTGGTGGAGTAATAAAACCACCCGCTATGGCTTCTCAAGGGCTCTTTCAGAA
TTTGGGAATAGAAGCAGTTCCTTGGACAGCAGGCAGCCCTTTAAAAGTAACTAGAATGTTCTCAAGTAGAGGTGAAAAAA
GGGCCACTTTGGAAACCTGCATATGACGTATTCCTGTACTTCTAGATATAAATTTGGATGAATAGAACTAAATATGTTTA
TTGGTAAAAAAGAATTCCAGAAACTAACGGCAGATCCCCGAAACCCAGACTTGTATCATGTATGAAGTGTTATCTGGCAA
GTAGCTTGTGAGATTAAGGTTCCGCACATGGAGGCTTGGTCGTCATTTGATGTATACACCCAAAATGGGCGGCTGGAAAA
CCCAAAGCGTAGGGAATTATTGGAGCTATTACAACAAAATCTGTATCTTACTCGAATGACTCCTCATGGAAATTTATTTA
CCGAGAACTTAACACCTATTAACTGTAATATATTTTTTCACATGTGAAAGCACTGTTTCGGGAGGCGCAGTGGCAATCTA
ATAGACCACTTAGGTTCATTGACTCCACTTGGTGCAATGGATATATTGATGCAAATAGGAAAAAAGGAAGAAGAGAAAAT
AACTAACATGTACCCTCAAGCCTTCAAAAAACTTTTTGAAACTATAGTGTTCCAAAGATTGTGC

Alignment

ORF - retro_ptro_2412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.22 %
• Parental protein coverage: 80.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDFKRYVTDRRLAETLAQIYLGKPSRPPHLLLECNPGPGILTQALLEAGAKVVALESDKTFIPHLESLGK
          LDFKRYVT.RRLAETLAQI...K..RPPHLLL.C.PGPGILTQALLE.GAKVVALESDKTFIPHLESLGK
Retrocopy LDFKRYVTNRRLAETLAQIVWRKQNRPPHLLLQCSPGPGILTQALLEVGAKVVALESDKTFIPHLESLGK

Parental  NLDGKLRVIHCDFFKLDPRSGGVIKPPAMSSRGLFKNLGIEAVPWTADIPLKVIGMFPSRGEKRALWKLA
          NLDGKL.VIHCDFFK.DPRSGGVIKPPAM.S.GLF.NLGIEAVPWTA..PLKV..MF.SRGEKRA.....
Retrocopy NLDGKLQVIHCDFFKIDPRSGGVIKPPAMASQGLFQNLGIEAVPWTAGSPLKVTRMFSSRGEKRATLETC

Parental  -YDLYSCTSIYKFGRIEVNMFIGEKEFQKLMADPGNPDLYHVLSVIWQLACEIKVLHMEPWSSFDIYTRK
          ....YSCTS.YKFG.IE.NMFIG.KEFQKL.ADP.NPDLYHV.SVIWQ.ACEIKV.HME.WSSFD.YT..
Retrocopy <HMTYSCTSRYKFG*IELNMFIGKKEFQKLTADPRNPDLYHV*SVIWQVACEIKVPHMEAWSSFDVYTQN

Parental  GPLENPKRRELLDQLQQKLYLIQMTPRQNLFTKNLTPMNYNIFFHLLKHCFGRRSATVIDHLRSLTPLDA
          G.LENPKRRELL..LQQ.LYL..MTP..NLFT.NLTP.N.NIFFH..KHCFGRRS...IDHL.SLTPL.A
Retrocopy GRLENPKRRELLELLQQNLYLTRMTPHGNLFTENLTPINCNIFFHM*KHCFGRRSGNLIDHLGSLTPLGA

Parental  RDILMQIGKQEDEKVVNMHPQDFKTLFETIERSKDC
          .DILMQIGK.E.EK..NM.PQ.FK.LFETI.....C
Retrocopy MDILMQIGKKEEEKITNMYPQAFKKLFETIVFQRLC

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	0.39 RPM	4.47 RPM
SRP007412_cerebellum	0.25 RPM	4.30 RPM
SRP007412_heart	0.09 RPM	7.26 RPM
SRP007412_kidney	0.08 RPM	12.79 RPM
SRP007412_liver	0.03 RPM	17.68 RPM
SRP007412_testis	0.21 RPM	6.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2412 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2412 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3548
Macaca mulatta	retro_mmul_1814

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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 ,