RetrogeneDB ID: retro_ptro_3028

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391837.1:2447315..2447851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSPTRG00000016009
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_ptro_3028
TGCCAGCAGCTGCCTACTGTTTATATCAGATCCCCACACGAGAACTTCAGGAAAAAGTTGATTGAAGAACTGAAGAGACA
AGAGGTAGTCCTAAAGGGTACTTCATGAAGCAGAGCATTGGGAACTTCTGTCACACAATTAGACTTATATAAGCAGTGGC
CGATAACCAAGACAAACCGAAATTTGAGGTGGGTCGATCCTAAAATATTTTATTTCTGAGGTGGAGAAAAATACCACTTG
TAGACAGCACAAAATCCTTTGAAAATAATAAGACCTTTCAGGCAGTTTATGATGCTATTGCATAGCAAGGCCAATGTCAG
GCAGATGACAAAGTGAATTTTTGTTTTATTCTGTTTAGCAACATGGATGGCCACCTCTCTGAACTTGATGGATGAATGCC
TTTCCCAGTGAACTATGGTGCCAGTTCAGAGGACTCACTGCTGCAGGACTGTAGAGATTAGGCTGCCAAGGTCTGTAGAA
AATTTACTGAGGAGGAAGGAGAGAAAGGCAGCCTCTCTGCTGTAACCCTCTCCAAG

Alignment

ORF - retro_ptro_3028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.09 %
• Parental protein coverage: 78.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CALLLLFPLTAQHENFRKKQIEELKGQEV-SPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFE-DGSVL
          C..L........HENFRKK.IEELK.QEV.SPK.YFMKQ.IGN.C.TI.LI.AVA.NQDK..FE..GS.L
Retrocopy CQQLPTVYIRSPHENFRKKLIEELKRQEV<SPKGYFMKQSIGNFCHTIRLI*AVADNQDKPKFE<GGSIL

Parental  KQFLSETEKMSP-EDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPV
          K.F.SE.EK.....D..K.FE.N...QA..DA.A..GQC..DDKVNF.FILF.N.DGHL.ELDG.MPFPV
Retrocopy KYFISEVEKNTT>VDSTKSFENNKTFQAVYDAIA*QGQCQADDKVNFCFILFSNMDGHLSELDG*MPFPV

Parental  NHGASSEDTLLKD----AAKVCREFTEREQGEVRFSAVALCK
          N.GASSED.LL.D....AAKVCR.FTE.E......SAV.L.K
Retrocopy NYGASSEDSLLQDCRD*AAKVCRKFTEEEGEKGSLSAVTLSK

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	627.29 RPM
SRP007412_cerebellum	0.00 RPM	156.01 RPM
SRP007412_heart	0.00 RPM	5.28 RPM
SRP007412_kidney	0.00 RPM	19.09 RPM
SRP007412_liver	0.00 RPM	5.11 RPM
SRP007412_testis	0.00 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3028 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3028 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_781

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Erinaceus europaeus	ENSEEUG00000002185	3 retrocopies	retro_eeur_150, retro_eeur_573, retro_eeur_598,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Homo sapiens	ENSG00000154277	2 retrocopies	retro_hsap_781, retro_hsap_782,
Gorilla gorilla	ENSGGOG00000008809	1 retrocopy	retro_ggor_648,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Myotis lucifugus	ENSMLUG00000010138	2 retrocopies	retro_mluc_1216, retro_mluc_2113,
Nomascus leucogenys	ENSNLEG00000017176	2 retrocopies	retro_nleu_2582, retro_nleu_2583,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Pan troglodytes	ENSPTRG00000016009	2 retrocopies	retro_ptro_3028 , retro_ptro_3029,
Tarsius syrichta	ENSTSYG00000008305	1 retrocopy	retro_tsyr_1191,