RetrogeneDB ID: retro_ptro_1949

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:176268960..176269724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BZW1
• Ensembl ID: ENSPTRG00000012791
• Aliases: None
• Description: None

Sequence

>retro_ptro_1949
CTAATGGCATCCATTCTTAATAGCCTTTATAATGAGAATTTGGTTAAAGAAGGGGTTTCAACAGCTTTTGCTGGAAAGCT
ATTTAAATCATGAATAAATGAAAAAGATATCAATGCAGTAACTGCAAGGAAAGTCAGCATGGATAACAGCCTGATGGAAC
TTTTTCCTGCCAATAAGCAAAGCGTTCAACACTTCACAAAGTATTTTACTGAGGCAGGCCTGAAAGAGCTTTCAGAATAT
GTTCGGAATCAGCAAACCATCAGAGCTTGTAAGGAGCTGCAGAAAGAACTTCAAGAACAGATGTCCCGTGGGGATCCATT
TAAGGTTATAATTTTATATGTCAAAGAGGAGATGAAAAAAAACAACATCCCAGAACCAGTTGTCATCGAAATAGTCTGGT
CAAATGTAATGAGCGCTGTGGAATGGAACAAAAGAGAGGAGATTGTAGCAGAGCAAGCCATCAAACACTTGAAGCAACAC
AGCCCTCTACTTGCTGCCTTTACTACTCAAGGTCAGTCTGAGCTGACTCTGTTACTGAAGATTCAGGAGTATTGCTATGA
CAACATTCATTTCATAAAAGCCTTCCAGAAAATAGTGGTGCTTTTTATAAAGCTGTAGTCCTGAGCAAAGAGCCCATTTT
GAAGTGGTATAAAGGTACACATGTTGCAAAGGGGAAGAGTGTTTTCCTTGAGCAAATGAAAAAGTTTGGAGAGTGGCTCA
AAAATGCTGAAGAAGAATCTGAATCTGAAGCTGAAGAAGTTGAC

Alignment

ORF - retro_ptro_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 56.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSMDNRLMELFPANKQSVEHFTKY
          L.ASILNSLYNENLVKEGVS.AFA.KLFKS.INEKDINAV.A..RKVSMDN.LMELFPANKQSV.HFTKY
Retrocopy LMASILNSLYNENLVKEGVSTAFAGKLFKS*INEKDINAVTA--RKVSMDNSLMELFPANKQSVQHFTKY

Parental  FTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMKKNNIPEPVVIGIVWSSVMS
          FTEAGLKELSEYVRNQQTI.A.KELQKELQEQMSRGDPFK.IILYVKEEM...NIPEPVVI.IVWS.VMS
Retrocopy FTEAGLKELSEYVRNQQTIRACKELQKELQEQMSRGDPFKVIILYVKEEMXXXNIPEPVVIEIVWSNVMS

Parental  TVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIHFMKAFQKIVVL-FYKAEV
          .VEWNK.EE.VAEQAIKHLKQ.SPLLAAFTTQGQSELTLLLKIQEYCYDNIHF.KAFQKIVVL.FYKA.V
Retrocopy AVEWNKREEIVAEQAIKHLKQHSPLLAAFTTQGQSELTLLLKIQEYCYDNIHFIKAFQKIVVL<FYKAVV

Parental  LSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD
          LS.EPILKWYK..HVAKGKSVFLEQMKKF.EWLKNAEEESESEAEE.D
Retrocopy LSKEPILKWYKGTHVAKGKSVFLEQMKKFGEWLKNAEEESESEAEEVD

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	0.04 RPM	56.02 RPM
SRP007412_cerebellum	0.00 RPM	57.50 RPM
SRP007412_heart	0.00 RPM	52.26 RPM
SRP007412_kidney	0.05 RPM	98.78 RPM
SRP007412_liver	0.00 RPM	83.57 RPM
SRP007412_testis	0.00 RPM	193.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1949 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1949 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2881
Gorilla gorilla	retro_ggor_1997
Macaca mulatta	retro_mmul_1457

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011878	1 retrocopy	retro_cfam_2150,
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus	ENSCPOG00000010449	1 retrocopy	retro_cpor_331,
Homo sapiens	ENSG00000082153	2 retrocopies	retro_hsap_2832, retro_hsap_2881,
Gorilla gorilla	ENSGGOG00000016296	1 retrocopy	retro_ggor_1997,
Mustela putorius furo	ENSMPUG00000012344	1 retrocopy	retro_mputfur_1174,
Mus musculus	ENSMUSG00000051223	3 retrocopies	retro_mmus_2499, retro_mmus_751, retro_mmus_990,
Nomascus leucogenys	ENSNLEG00000006929	1 retrocopy	retro_nleu_621,
Pan troglodytes	ENSPTRG00000012791	1 retrocopy	retro_ptro_1949 ,