RetrogeneDB ID: retro_ptro_2021

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:148363069..148363762(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041132
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RTN3
• Ensembl ID: ENSPTRG00000003809
• Aliases: None
• Description: Pan troglodytes reticulon 3 (RTN3), mRNA. [Source:RefSeq mRNA;Acc:NM_001048049]

Sequence

>retro_ptro_2021
ATGGCGGAGCCATCGGCGGCCACTCAGTCCCCTTCCATCTCCTCGTCGTACTCGGGAGCCAAGGCGTCCGCGCCCGGCAG
CAGCGGAAGCCCAGGAGCCTGCCCTGCCCTGGGGACGAAGAGCTGCAGCTCCTCCTGTGCGGTTCACGATCTGATTTTCT
GGAGAGATGTGAAGAAGACTGGGTTTGTCTTTGCCACCACGCTGATAATGCTGCTTTCCCTGGCAGCTTTCAGTGTCATC
AGTGTGGTTTCTTACCTCATCCTGGCTCTTCTCTCTGTCACCATCAGCTTCAGGATCTACAAGTCCGTCATCCAAGCTGT
ACAGAAGTCAGAAGAAGGCCATCCATTCAAATCCTACCTGGACGTAGACATTACTCTGTCCTCGGAAGCTTTCCATAATT
ACATGAATGCTGCCATGGTGCACATCAACACGGCCCCGAAACTCATTATTTGTCTCTTTCTGGTAGAAGATCTGGTTGAC
TCCTTGAAGCTGGCTGTCTTCATGTGGCTGATGACCTATGTTGGTGCTGTTTTTAACGGAATCACCCTTCTAATTCTTGC
TGAACTGCTCATTTTCAGTGTCCCGATTGTCTATGAGAAGTACAAGACCCAGATTGATCACTATGTTGGCATCGCCTGAG
ATCAGACCAAGTCAATTGTTGAAAAGATCCAAGCAAAACTCCCTGGAATTGCC

Alignment

ORF - retro_ptro_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 97.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEPSAATQSHSISSSSFGAEPSAPGGGGSPGACPALGTKSCSSSCAVHDLIFWRDVKKTGFVFGTTLIM
          MAEPSAATQS.SISSS..GA..SAPG..GSPGACPALGTKSCSSSCAVHDLIFWRDVKKTGFVF.TTLIM
Retrocopy MAEPSAATQSPSISSSYSGAKASAPGSSGSPGACPALGTKSCSSSCAVHDLIFWRDVKKTGFVFATTLIM

Parental  LLSLAAFSVISVVSYLILALLSVTISFRIYKSVIQAVQKSEEGHPFKAYLDVDITLSSEAFHNYMNAAMV
          LLSLAAFSVISVVSYLILALLSVTISFRIYKSVIQAVQKSEEGHPFK.YLDVDITLSSEAFHNYMNAAMV
Retrocopy LLSLAAFSVISVVSYLILALLSVTISFRIYKSVIQAVQKSEEGHPFKSYLDVDITLSSEAFHNYMNAAMV

Parental  HINRALKLIIRLFLVEDLVDSLKLAVFMWLMTYVGAVFNGITLLILAELLIFSVPIVYEKYKTQIDHYVG
          HIN.A.KLII.LFLVEDLVDSLKLAVFMWLMTYVGAVFNGITLLILAELLIFSVPIVYEKYKTQIDHYVG
Retrocopy HINTAPKLIICLFLVEDLVDSLKLAVFMWLMTYVGAVFNGITLLILAELLIFSVPIVYEKYKTQIDHYVG

Parental  IARDQTKSIVEKIQAKLPGIA
          IA.DQTKSIVEKIQAKLPGIA
Retrocopy IA*DQTKSIVEKIQAKLPGIA

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	1.61 RPM	657.26 RPM
SRP007412_cerebellum	0.22 RPM	221.79 RPM
SRP007412_heart	0.00 RPM	26.09 RPM
SRP007412_kidney	0.18 RPM	75.81 RPM
SRP007412_liver	0.03 RPM	49.43 RPM
SRP007412_testis	0.11 RPM	79.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2021 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2021 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2021 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2988

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000133318	1 retrocopy	retro_hsap_2988,
Pan troglodytes	ENSPTRG00000003809	1 retrocopy	retro_ptro_2021 ,