RetrogeneDB ID: retro_ptro_444

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:78459285..78459984(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGGT1B
• Ensembl ID: ENSPTRG00000017146
• Aliases: None
• Description: None

Sequence

>retro_ptro_444
CAGGTCTTTCCCACAGAAGACAGATCAAATCTAAATCGCTGTGGTTTCCGAGGCTCTTCATACCTGGGTATTCTGTTCAA
TCCATCAAAGGCTCCTGGAACAGCTCATCCTTATGATAGTGGCCACATTGCAATGACCTACACTGGCCTTTCATGCTTAC
TTATTCTTGGAGACGACTTAAGCCGAGTAAATAAAGAAGCTTGCTTAGCAGGCTTGAGAGCCCTTCAGCTGGAAGATGGG
AGTTTTTGTGCAGTACCTGAAGGCAGTGAAAATGACATGCGATTTTTGTACTGTACTTCCTGTATTTGCTATATGCTCAA
CAACCGGTCAGGCATGGATATGAAAAAAGCCATCTCCTATATTAGAAGAAGTATGTCCTATGACAATGGACTGGCACAGG
GAGCTGGACTTGAATCTCATGGAGGATCTACTTTTTGTGCCATTGCCTCACTATGTCTGATGGGTAAACTAGAAGAAGTT
TTTTCAGAAAAAGAATTGAACAGGATAAAGAGGTGGTGTATGAGGCAACAAAATAGTTATCGTGGAAGACCTAATAAGCC
TGTAGACACCGGTTATTCTTTTTGGGTGGGAGCAACTCTAAAGCTTCTAAAAATTTTCCAATACACTAACTTTGAGAAAA
ATAGAAATTACATCTTATCAACTCAAGATCGCCTTGTAGGGGGATTTGCCAAGTGGCCA

Alignment

ORF - retro_ptro_444 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.87 %
• Parental protein coverage: 62.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVLPTEDRSNLNRCGFRGSSYLGIPFNPSKAPGTAHPYDSGHIAMTYTGLSCLVILGDDLSRVNKEACLA
          QV.PTEDRSNLNRCGFRGSSYLGI.FNPSKAPGTAHPYDSGHIAMTYTGLSCL.ILGDDLSRVNKEACLA
Retrocopy QVFPTEDRSNLNRCGFRGSSYLGILFNPSKAPGTAHPYDSGHIAMTYTGLSCLLILGDDLSRVNKEACLA

Parental  GLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNNWSGMDMKKAITYIRRSMSYDNGLAQGAGLESH
          GLRALQLEDGSFCAVPEGSENDMRF.YC.SCICYMLNN.SGMDMKKAI.YIRRSMSYDNGLAQGAGLESH
Retrocopy GLRALQLEDGSFCAVPEGSENDMRFLYCTSCICYMLNNRSGMDMKKAISYIRRSMSYDNGLAQGAGLESH

Parental  GGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKPVDTCYSFWVGATLKLLKIFQYT
          GGSTFC.IASLCLMGKLEEVFSEKELNRIKRWC.MRQQN.Y.GRPNKPVDT.YSFWVGATLKLLKIFQYT
Retrocopy GGSTFCAIASLCLMGKLEEVFSEKELNRIKRWC-MRQQNSYRGRPNKPVDTGYSFWVGATLKLLKIFQYT

Parental  NFEKNRNYILSTQDRLVGGFAKWP
          NFEKNRNYILSTQDRLVGGFAKWP
Retrocopy NFEKNRNYILSTQDRLVGGFAKWP

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	2.32 RPM
SRP007412_cerebellum	0.04 RPM	6.60 RPM
SRP007412_heart	0.00 RPM	10.11 RPM
SRP007412_kidney	0.00 RPM	7.01 RPM
SRP007412_liver	0.03 RPM	5.20 RPM
SRP007412_testis	0.21 RPM	9.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_444 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_444 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_675
Pan troglodytes	retro_ptro_487
Homo sapiens	retro_hsap_698

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016700	1 retrocopy	retro_cjac_1058,
Cavia porcellus	ENSCPOG00000002443	1 retrocopy	retro_cpor_1344,
Homo sapiens	ENSG00000164219	2 retrocopies	retro_hsap_675, retro_hsap_698,
Loxodonta africana	ENSLAFG00000003752	1 retrocopy	retro_lafr_668,
Pongo abelii	ENSPPYG00000015694	3 retrocopies	retro_pabe_527, retro_pabe_545, retro_pabe_640,
Pan troglodytes	ENSPTRG00000017146	2 retrocopies	retro_ptro_444 , retro_ptro_487,