RetrogeneDB ID: retro_pabe_545

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:85509589..85510293(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGGT1B
• Ensembl ID: ENSPPYG00000015694
• Aliases: None
• Description: protein geranylgeranyltransferase type I, beta subunit [Source:HGNC Symbol;Acc:8895]

Sequence

>retro_pabe_545
ATGCAGGTCCTTCCCACAGAAGACAGATCAAATCTAAATCTCTGTGGTTTCCGAGGCTCTTCAAACCTGGGTATTCCGCT
CAATCCATCAAAGGCTCCTGGAACAGCTCATCCTTATGATAGTGGCCACATTGCAATGACTTACACTGGCCTTTCATGCT
TAGCTATTCTTGGAGACGACTTAAGCCGGGTAAATAAAGAAGCTTGCTTAGCAGGCTTGAGAGCCCTTCAGCTGGAAGAT
GGGAGTTTTTGTGCAGTAACTGAAGGCAGTGAAAATGACATGCGATTTTTGTACTGTACTTCCTGTATTTGCTATATGCT
CAACAACCGGTCAGGCATGGATATGAAAAAAGCCATCTCCTATATTAAAAGAAGTATGTCCTACGGCAATGGACTGGCAC
AGGGAGCTGGACTTGAATCTCATGGAGGATCTACTTTTTGTGCCTTGCCTCACTATGTCTGATGGGTAAACTAGAAGAAG
TTTTTTCAGAAAAAGAATTGAACAGGATAAAGGGGTGGTGTATAATGAGGCAACAAAATAGTTATCATGGAAGACCTATT
AAGCCTGTAGACACCTGTTATTCTTTTTGGGTGGGAGCAACTCTAAAGCTTCTAAAAATTTTCCAATACACTAAGTTTGA
GAAAAACAGAAATTCCATCTTATCAACTCAAGATTGCCTCACAGGGGGATTTGCCAAGTGGCCA

Alignment

ORF - retro_pabe_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 62.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQVLPTEDRSNLNRCGFRGSSYLGIPFNPSKAPGTAHPYDSGHIAMTYTGLSCLVILGDDLSRVNKEACL
          .QVLPTEDRSNLN.CGFRGSS.LGIP.NPSKAPGTAHPYDSGHIAMTYTGLSCL.ILGDDLSRVNKEACL
Retrocopy MQVLPTEDRSNLNLCGFRGSSNLGIPLNPSKAPGTAHPYDSGHIAMTYTGLSCLAILGDDLSRVNKEACL

Parental  AGLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNNWSGMDMKKAMHPILGERMSYDNGLAQGAGLE
          AGLRALQLEDGSFCAV.EGSENDMRF.YC.SCICYMLNN.SGMDMKKA........MSY.NGLAQGAGLE
Retrocopy AGLRALQLEDGSFCAVTEGSENDMRFLYCTSCICYMLNNRSGMDMKKAI-SYIKRSMSYGNGLAQGAGLE

Parental  SHGGSTFCG-IASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKPVDTWYSFWVGATLKLLKIF
          SHGGSTFC...ASLCLMGKLEEVFSEKELNRIK.WCIMRQQN.YHGRP.KPVDT.YSFWVGATLKLLKIF
Retrocopy SHGGSTFCA<LASLCLMGKLEEVFSEKELNRIKGWCIMRQQNSYHGRPIKPVDTCYSFWVGATLKLLKIF

Parental  QYTNFEKNRNYILSTQDRLVGGFAKWP
          QYT.FEKNRN.ILSTQD.L.GGFAKWP
Retrocopy QYTKFEKNRNSILSTQDCLTGGFAKWP

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	2.21 RPM
SRP007412_cerebellum	0.24 RPM	2.80 RPM
SRP007412_heart	0.03 RPM	4.00 RPM
SRP007412_kidney	0.23 RPM	5.44 RPM
SRP007412_liver	0.03 RPM	3.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_545 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_545 has 0 orthologous retrocopies within eutheria group .

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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,