RetrogeneDB ID: retro_pabe_2642

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:67601096..67601474(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCL1B
• Ensembl ID: ENSPPYG00000006118
• Aliases: None
• Description: T-cell leukemia/lymphoma 1B [Source:HGNC Symbol;Acc:11649]

Sequence

>retro_pabe_2642
ATGGCCTCCGAAGCTTCTCTGCATCTCAGGGCACCCCCTGAACTGTCTGTGGATCTGGAGGCCTGGCATCTATGAGGATG
ACTAGGGGAGGACCTGGGTGACTGTGGTTGTGCACCTCAGTCCCCTGCACAGAGAAAGGGCCGGGTGCTCGAGCTCCCAG
GGCAGCACATACGAACCTAGCATCACGGTGCACATGTGGCAGATGCCAGTGCACACCCAGGAGCCACTGTCCTCCAGCCA
GCTGCCCTTCTCCCACCTGCTCCCCGTGTGGCAGCTCACCCCAAGAGGAGGTACCAAGCAGCAAATTCCAGTTTCTAGGA
AATAGTGGACCAGATCGTCTCCGTGGAGCAGCTGGTCCTAACATATTGGCCGGCAAGG

Alignment

ORF - retro_pabe_2642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.15 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASEASVRLGVPPDR-LWIRRPGIYEDEEGRTWVTVVVRFNPSHREWA--RASQGSRYEPSITVHLWQLA
          MASEAS..L..PP...LWI.RPGIYED..GRTWVTVVV...P.HRE.A....SQGS.YEPSITVH.WQ..
Retrocopy MASEASLHLRAPPEL>LWIWRPGIYEDD*GRTWVTVVVHLSPLHRERAGCSSSQGSTYEPSITVHMWQMP

Parental  VHTREPLSSGQMPFSQLPAVWQL-YPGKKYRAADSSFWEIADHGQIDSMEQLVLTYQPER
          VHT.EPLSS.Q.PFS.L..VWQL..P...Y.AA.SSF.EI.D..QI.S.EQLVLTY.P.R
Retrocopy VHTQEPLSSSQLPFSHLLPVWQL<HPKRRYQAANSSF*EIVD--QIVSVEQLVLTYWPAR

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.07 RPM	0.00 RPM
SRP007412_liver	0.09 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2642 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2642 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3183
Pan troglodytes	retro_ptro_2261

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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,