RetrogeneDB ID: retro_pabe_2860

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:38644098..38644784(+)
• Located in intron of: ENSPPYG00000016567

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSPPYG00000013597
• Aliases: None
• Description: TRK-fused gene [Source:HGNC Symbol;Acc:11758]

Sequence

>retro_pabe_2860
GAAGATGACGATCTTTCCTTTGCAATTCAGTGTAGTAGGATACCGAAATTGACATTATTTGTTAATGGCCAACCAAGACC
CCTTGAATCAAGTCAGGTAAAATATCTCTGTCGAGAACTGACAGAACTTTGAAATAAAGTGAATCATTTATTGGATAGCT
TGGAACCACCTGGAGAACCAGGACTTTCCACCAATATTCCTGAAAATGTTACTGTGAATGGTAGGGAAGAAAAGCCTGCT
TCTTCGGATTCTTCTGGAAAACAGTCTATTCAGGTTATGACAGCAAGTATGTCAGCTTTCGACCCTTTAAAAAAACCAAG
ATGAAATAAAAAATAATGTTACGTCGGCATTTGGCTTAACAGATGATCAGGTTTCAGGGAAACCCAGTGCTCTTGCAGAA
GACTGTTCAGGAACATCTGACAGCATTGCCGCCTCCTCCTCAGTAGCAGCTCACCCACCAGGAGTTCAGCCACAGCAACC
ACCATATACAGAAGCTAAGATACAAGGAGGTCAGACTGAAAGTCAGCTGTACCAACAGTAGCAGCAACAGGCTAGCTATG
GTGCGCAGCGTCTGTGGGCTCCACCTCAGCAGCCTCAACAGTATGGTATTCAGTATTCAAAAAGCCAGCGTCAGCAGACT
GGACCCCAAACAACCTCAGCAGTTCCAAGGATATGGCCAGCAACCA

Alignment

ORF - retro_pabe_2860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.3 %
• Parental protein coverage: 56.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSSDLSFAIQCSRILKLTLFVNGHPRPLESSQVKYLRRELIELRNKVNRLLDSLEPPGEPGPSTTIPEND
          ...DLSFAIQCSRI.KLTLFVNG.PRPLESSQVKYL.REL.EL.NKVN.LLDSLEPPGEPG.ST.IPEN.
Retrocopy EDDDLSFAIQCSRIPKLTLFVNGQPRPLESSQVKYLCRELTEL*NKVNHLLDSLEPPGEPGLSTNIPENV

Parental  TVDGREEKSA-SDSSGKQSTQVMAASMSAFDPL-KNQDEINKNVMSAFGLTDDQVSGPPSAPAEDRSGTP
          TV.GREEK.A.SDSSGKQS.QVM.ASMSAFDPL.KNQDEI..NV.SAFGLTDDQVSG.PSA.AED.SGT.
Retrocopy TVNGREEKPASSDSSGKQSIQVMTASMSAFDPL>KNQDEIKNNVTSAFGLTDDQVSGKPSALAEDCSGTS

Parental  DSIASSSS-AAHPPGVQPQQPPYTGAQTQAGQIEGQMYQQYQQQAGYGAQQPQAPPQQPQQYGIQYSASY
          DSIA.SSS.AAHPPGVQPQQPPYT.A..Q.GQ.E.Q.YQQ.QQQA.YGAQ...APPQQPQQYGIQYS.S.
Retrocopy DSIAASSSVAAHPPGVQPQQPPYTEAKIQGGQTESQLYQQ*QQQASYGAQRLWAPPQQPQQYGIQYSKSQ

Parental  SQQTGPQ-QPQQFQGYGQQP
          .QQTGPQ.QPQQFQGYGQQP
Retrocopy RQQTGPQ>QPQQFQGYGQQP

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	0.06 RPM	22.89 RPM
SRP007412_cerebellum	0.00 RPM	34.53 RPM
SRP007412_heart	0.03 RPM	17.70 RPM
SRP007412_kidney	0.10 RPM	29.17 RPM
SRP007412_liver	0.03 RPM	49.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2860 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2860 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3459
Pan troglodytes	retro_ptro_2345
Macaca mulatta	retro_mmul_1760

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860 ,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,