RetrogeneDB ID: retro_ptro_3086

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL396799.1:2..911(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: URI1
• Ensembl ID: ENSPTRG00000010784
• Aliases: None
• Description: Chromosome 19 open reading frame 2 [Source:UniProtKB/TrEMBL;Acc:K7CIT3]

Sequence

>retro_ptro_3086
GCAAATGGAGAAGATACGACATCTTCTGAAGAGGAAAAGGAAGATCGTAACACAAATGTGAATGCGATGCATCAAGTAAC
AGACTCTCATACTCCTTGTCATAAGGATGTTGCAAGTTCAGAACCATTCAGTGGTCAAGTGAATAGTCAGTTGAACTGTT
CAGTGAAGGGTTCCAGTTCTTACCACAGTGATGATGATGATGATGATGATGATGATGATGATGACGACGACGACGACAAC
ATTGACGACAATGATGGTGATAATGACCATGAGGCTTTAGGGGTTGGAGATAATTCTATACCAACAATATATTTTTCACA
TACTGTTGAGCCTAAGAGGGTCCGAATAAATACTGGAAAGAATACCACTTTAAAATTCAGTGAAAAGAAAGAAGAAGCCA
AACGTAAATGAAAGAACAGCACTGGCAGTGGCCACTCTGCCCAGGAGCTGCCGACCATCAGGACGCCTGCAGACATTTAC
AGAGCCTTTGTTGATGTTGTGAATGGAGAATATGTCCCTCGCAAATCCATCCTGAAGTCTCGAAGTAGAGAGAATAGTGT
GTGTAGCGACACCAGTGAAAGCAGTGCTGCTGAATTTGATGATAGGCGGGGAGTTTTGAGGAGTATCAGCTGCGAAGAAG
CCACTTGCAGTGACACCAGTGAGAGCATTTTGGAAGAGGAACCACAAGAAAATCAAAAGAAACTTTTGCCCTTATCAGTA
ACACCTGAGGCTTTTTCTGGAACTGTTTTGGAAAAAGAATTTGTATCACCTTCCTTAACACCACACCCAGCCATTGCTCA
TCCTGCACTACCCACTATTCCAGAACGAAAGGAAGTTCTGTTGGAAGCATCAGAAGAAACTGGAAAGAGGGTTTCAAAGT
TTAAAGCTGCCAGATTGCAACAGAAAAAC

Alignment

ORF - retro_ptro_3086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.07 %
• Parental protein coverage: 57.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANGEDTTSSEEEKEDRNTNVNAMHQVTDSHTPCHKDVASSEPFSGQVNSQLNCSVNG-SSSYHSDDDDDD
          ANGEDTTSSEEEKEDRNTNVNAMHQVTDSHTPCHKDVASSEPFSGQVNSQLNCSV.G.SS..........
Retrocopy ANGEDTTSSEEEKEDRNTNVNAMHQVTDSHTPCHKDVASSEPFSGQVNSQLNCSVKGSSSYHXXXXXXXX

Parental  DEDDDDDDDNIDDDGGDNDHEALGVGDNSIPTIYFSHTVEPKRVRINTGKNTTLKFSEKKEEAKRKRKNS
          .....DDDDNIDD..GDNDHEALGVGDNSIPTIYFSHTVEPKRVRINTGKNTTLKFSEKKEEAKRK.KNS
Retrocopy XXXXXDDDDNIDDNDGDNDHEALGVGDNSIPTIYFSHTVEPKRVRINTGKNTTLKFSEKKEEAKRK*KNS

Parental  TGSGHSAQELPTIRTPADIYRAFVDVVNGEYVPRKSILKSRSRENSVCSDTSESSAAEFDDRRGVLRSIS
          TGSGHSAQELPTIRTPADIYRAFVDVVNGEYVPRKSILKSRSRENSVCSDTSESSAAEFDDRRGVLRSIS
Retrocopy TGSGHSAQELPTIRTPADIYRAFVDVVNGEYVPRKSILKSRSRENSVCSDTSESSAAEFDDRRGVLRSIS

Parental  CEEATCSDTSESILEEEPQENQKKLLPLSVTPEAFSGTVIEKEFVSPSLTPHPAIAHPALPTIPERKEVL
          CEEATCSDTSESILEEEPQENQKKLLPLSVTPEAFSGTV.EKEFVSPSLTPHPAIAHPALPTIPERKEVL
Retrocopy CEEATCSDTSESILEEEPQENQKKLLPLSVTPEAFSGTVLEKEFVSPSLTPHPAIAHPALPTIPERKEVL

Parental  LEASEETGKRVSKFKAARLQQKN
          LEASEETGKRVSKFKAARLQQKN
Retrocopy LEASEETGKRVSKFKAARLQQKN

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	1.13 RPM	25.02 RPM
SRP007412_cerebellum	0.36 RPM	24.66 RPM
SRP007412_heart	0.12 RPM	17.46 RPM
SRP007412_kidney	0.68 RPM	29.13 RPM
SRP007412_liver	0.59 RPM	16.11 RPM
SRP007412_testis	0.63 RPM	69.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3086 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3086 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001823	1 retrocopy	retro_cjac_2693,
Monodelphis domestica	ENSMODG00000012675	1 retrocopy	retro_mdom_1513,
Pongo abelii	ENSPPYG00000009810	1 retrocopy	retro_pabe_547,
Pan troglodytes	ENSPTRG00000010784	1 retrocopy	retro_ptro_3086 ,