RetrogeneDB ID: retro_ptro_1320

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:20587415..20588461(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000033914
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTR2
• Ensembl ID: ENSPTRG00000011990
• Aliases: None
• Description: ARP2 actin-related protein 2 homolog [Source:UniProtKB/TrEMBL;Acc:K7C293]

Sequence

>retro_ptro_1320
AAAGTGGGAAACATTGAAATCAAGGATCTTATGGTTGGTGATGAGGCAAGTGAATTACGATCAGTGTTAGAAGTTAACTA
CCCTATGGAAAATGGCATAGTACGAAATTGGGATGACACGCAACACCTGTGGGACTACACATTTGGACCAGAGAAACCTA
ATATAGATACCAGAAATTGTAAAATCTTACTCACAGAACCTCTTATGAACCCAACCGAAAACAGAGAGAAGATGGTAGAG
GTAATGTTTGAAACTTACCAGTTTTCCGGTATATATGTAGCCATCCAGGCAGTTCTGACTTTGTACGCTCAAGGTTTATT
GACTGGTGTAGTGGTAGACTCTGGAGATGGCGTGACTCACATTTACCCAGTATATGAAGGCTTTTCTCTCCCTCATCTTA
CCAGGAGACTGGATATTGCTGGGAGGGATATAACTAGATATCTTATCAAGCTACTTCTGTTGCAAGGATACACCTTCAAC
CACTCTGCTGATTTTGAAACGGTTCGCATGATTAAAGAAAAACTGTGTTACGTGGGATATAATATTGTGCAAGAGCAGAA
ACTGGCCTTAGAAACCACAGTATTAGTTGAATCTTATACACTCCCAGATGGATGAATCATCAAAGTTGGGGGAGAGAGAT
TTGAAACACCAGAAGCTTTATTTCAGCCTCACTTGATCAATGTTGAAGGAGTTGGTGTTGCTGAATTGCTTTTTAACACA
ATTCAGGCGGCTGACATTGATACCAGATCTGAATTCTACAAACACATTGTGCTTTCTGGAGGGTCTACTATGTATCCTGG
CCTGTCATCATGGTTGAACGAGAACTTAAACAGCTTTACTTAGAAAGAGTTTTGAAGGATGATGTGGAAAAACTTCCTAA
ATTTAAGATCTGCATTGAAGACCCATCCCGCAGAAAGCACATGGTATTCTTGGGCGGTGCAGTTCTAGTGGATATCATGA
AAGACAAAGACAATTTTTGGATGACCCGACAGGAGTACCAAGAAAAGGGTGTCCTTGTGCTAAAGAAACTTGGTGTGACT
GTTCGA

Alignment

ORF - retro_ptro_1320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.14 %
• Parental protein coverage: 87.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIKNNKKMDLMVGDEASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMN
          ...N....DLMVGDEASELRS.LEVNYPMENGIVRNWDD..HLWDYTFGPEK.NIDTRNCKILLTEP.MN
Retrocopy KVGNIEIKDLMVGDEASELRSVLEVNYPMENGIVRNWDDTQHLWDYTFGPEKPNIDTRNCKILLTEPLMN

Parental  PTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIA
          PT.NREK.VEVMFETYQFSG.YVAIQAVLTLYAQGLLTGVVVDSGDGVTHI.PVYEGFSLPHLTRRLDIA
Retrocopy PTENREKMVEVMFETYQFSGIYVAIQAVLTLYAQGLLTGVVVDSGDGVTHIYPVYEGFSLPHLTRRLDIA

Parental  GRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGRIIKVG
          GRDITRYLIKLLLL.GY.FNHSADFETVRMIKEKLCYVGYNI.QEQKLALETTVLVESYTLPDG.IIKVG
Retrocopy GRDITRYLIKLLLLQGYTFNHSADFETVRMIKEKLCYVGYNIVQEQKLALETTVLVESYTLPDG*IIKVG

Parental  GERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRL-ERELKQL
          GERFE.PEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGL.S.L.ERELKQL
Retrocopy GERFETPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLSSWL<ERELKQL

Parental  YLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR
          YLERVLK.DVEKL.KFKI.IEDP.RRKHMVFLGGAVL.DIMKDKDNFWMTRQEYQEKGV.VL.KLGVTVR
Retrocopy YLERVLKDDVEKLPKFKICIEDPSRRKHMVFLGGAVLVDIMKDKDNFWMTRQEYQEKGVLVLKKLGVTVR

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	0.88 RPM	155.69 RPM
SRP007412_cerebellum	2.40 RPM	231.51 RPM
SRP007412_heart	0.73 RPM	114.49 RPM
SRP007412_kidney	0.84 RPM	113.50 RPM
SRP007412_liver	0.82 RPM	116.04 RPM
SRP007412_testis	1.48 RPM	103.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1320 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1320 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009761	1 retrocopy	retro_btau_707,
Callithrix jacchus	ENSCJAG00000006722	1 retrocopy	retro_cjac_429,
Homo sapiens	ENSG00000138071	1 retrocopy	retro_hsap_1978,
Gorilla gorilla	ENSGGOG00000008505	1 retrocopy	retro_ggor_1435,
Monodelphis domestica	ENSMODG00000003364	2 retrocopies	retro_mdom_1082, retro_mdom_754,
Mus musculus	ENSMUSG00000020152	1 retrocopy	retro_mmus_2989,
Pongo abelii	ENSPPYG00000012359	1 retrocopy	retro_pabe_1877,
Pan troglodytes	ENSPTRG00000011990	1 retrocopy	retro_ptro_1320 ,