RetrogeneDB ID: retro_ptro_2261

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:49303232..49303617(-)
• Located in intron of: ENSPTRG00000016935

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCL1B
• Ensembl ID: ENSPTRG00000006694
• Aliases: None
• Description: T-cell leukemia/lymphoma 1B [Source:HGNC Symbol;Acc:11649]

Sequence

>retro_ptro_2261
ATGGCCTCCAAAACTTCTCCGCATCTCAGGGCACCCCCCCAACTGTCTGTGGATCTGGAGGCCTGGCATCTATGAGGATG
ACAAGGGGAGGACCTGGGTGACTGTGGTTGTGCGCCTCAGTCCCCTGCACAGAGAAAGGGCCAGGTGCTCAAGCTCCCAG
GGCAGCACATATGAACCTAGCATCACAGTGCACATGTGGTAGATGCCAGTGCACACCCGGGAGCCACTGTCCCCCAGCCA
GCTGCCCTTCTCCCACCTGCTCCCTGTGTGGCAGCTCTACCCCAAGAGGAGGTATCAAGCAGCAAATTCCAGTTTCTGGG
AAATAGTGGACCAGATCATCTCCATGGAGCAGCTGGTCCTAACATATTGGCCGGCAAGGAATAAC

Alignment

ORF - retro_ptro_2261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASEASVRL-GVPPGRLWIQRPGIYEDEEGRTWVTVVVRFNPSHREWAR--ASQGSRYEPSITVHLWQMA
          MAS..S..L.G.PP..LWI.RPGIYED..GRTWVTVVVR..P.HRE.AR...SQGS.YEPSITVH.W.M.
Retrocopy MASKTSPHL>GHPPNCLWIWRPGIYEDDKGRTWVTVVVRLSPLHRERARCSSSQGSTYEPSITVHMW*MP

Parental  VHTRELLSSGQMPFSQLPAVWQLYPGRKYRAADSSFWEIADHGQIDSMEQLVLTYQPERKD
          VHTRE.LS..Q.PFS.L..VWQLYP.R.Y.AA.SSFWEI.D..QI.SMEQLVLTY.P.R..
Retrocopy VHTREPLSPSQLPFSHLLPVWQLYPKRRYQAANSSFWEIVD--QIISMEQLVLTYWPARNN

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	0.02 RPM	0.00 RPM
SRP007412_cerebellum	0.07 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.08 RPM	1.99 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.11 RPM	0.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2261 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2261 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3183
Pongo abelii	retro_pabe_2642

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000213231	1 retrocopy	retro_hsap_3183,
Gorilla gorilla	ENSGGOG00000013671	1 retrocopy	retro_ggor_1341,
Mus musculus	ENSMUSG00000060863	2 retrocopies	retro_mmus_1150, retro_mmus_1605,
Nomascus leucogenys	ENSNLEG00000000495	1 retrocopy	retro_nleu_1660,
Pongo abelii	ENSPPYG00000006118	1 retrocopy	retro_pabe_2642,
Pan troglodytes	ENSPTRG00000006694	1 retrocopy	retro_ptro_2261 ,