RetrogeneDB ID: retro_ptro_2022

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:150504357..150505037(+)
• Located in intron of: ENSPTRG00000016494

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSPTRG00000005840
• Aliases: None
• Description: None

Sequence

>retro_ptro_2022
CAGGTTCCTGAATATTTGTCACAGCAATGAGCTAAAGCCCCTGGAAGAGGTGAAGTTGGGAAACTGTGGATTGCCAAGAC
TCAAGGAAGGACTGAGGTGTCATTTACTTTGAATGAAGATCTTGCAAATATTCATGATATTGGCCGAAAAGCAGCTTCAG
TCAGTGCTCATAAAGAACACCCGTTTGTCTTGCAAAATTTTGGAGGCCATATATGAACAATATTTACTGAGAGCTCATCA
GATAAGCTGTCTTCGGAAGGAATAGTGGTACAAAGAACTGAATGCCAACAGACTGCCAGTGAAAAGTACATGAGATTAAA
AAGATTGCAAATAGAGGAATCTTCCAAACATGTAAGGCTATCACAACAACTGGACAAAGTTGTAACAGCCAGTTTTGAAT
CTGTTGCTAATCAATACAATACTGAATGTGAAAGGAAAGAGAAAGCAGATGGAAAATAAGCTCCAGCTAATAAACAACAC
GTTTCAGACATGCTATTTTCAGCCTTTAGAAATATCAATATTATCATCTTAAGGACTTGGTGGACATCACAAAACAACCT
GTGGTATACCTGAGGGAACTCTTAAAAGAAATTGGTCTTCAGAATGTAAAAGAGATCCACAAAAACACGTGGGAGCTGAA
ACCAGAGTACAGACATCACCAAGGAGAAGAAATGAGTGAT

Alignment

ORF - retro_ptro_2022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.91 %
• Parental protein coverage: 91.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVPKYLSQQWAKASGRGEVGKLRIAKTQGRTEVSFTLNEDLANIHDIGGKPASVSAPREHPFVLQSVGGQ
          .VP.YLSQQ.AKA.GRGEVGKL.IAKTQGRTEVSFTLNEDLANIHDIG.K.ASVSA..EHPFVLQ..GG.
Retrocopy QVPEYLSQQ*AKAPGRGEVGKLWIAKTQGRTEVSFTLNEDLANIHDIGRKAASVSAHKEHPFVLQNFGGH

Parental  TLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANHQY
          ..T.FTESSSDKLS.EGIVVQR.EC...ASE.YMRLKRLQIEESSK.VRLSQQLDKVVT.....VAN.QY
Retrocopy I*TIFTESSSDKLSSEGIVVQRTECQQTASEKYMRLKRLQIEESSKHVRLSQQLDKVVTASFESVAN-QY

Parental  NIEYERKKKEDGKRARADKQHVLDMLFSAFE-KHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHK
          N.E.ERK.K.DGK.A.A.KQHV.DMLFSAF..K.QYY.LKDLVDITKQPVVYL.E.LKEIG.QNVK.IHK
Retrocopy NTECERKEKADGK*APANKQHVSDMLFSAFR<KYQYYHLKDLVDITKQPVVYLRELLKEIGLQNVKEIHK

Parental  NTWELKPEYRHYQGEEKSD
          NTWELKPEYRH.QGEE.SD
Retrocopy NTWELKPEYRHHQGEEMSD

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	0.02 RPM	7.53 RPM
SRP007412_cerebellum	0.04 RPM	6.63 RPM
SRP007412_heart	0.03 RPM	7.72 RPM
SRP007412_kidney	0.00 RPM	8.39 RPM
SRP007412_liver	0.00 RPM	6.58 RPM
SRP007412_testis	0.00 RPM	19.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2022 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2022 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2990
Gorilla gorilla	retro_ggor_2070
Macaca mulatta	retro_mmul_1913

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Callithrix jacchus	ENSCJAG00000019220	2 retrocopies	retro_cjac_1351, retro_cjac_2990,
Homo sapiens	ENSG00000188342	2 retrocopies	retro_hsap_2990, retro_hsap_368,
Gorilla gorilla	ENSGGOG00000006657	2 retrocopies	retro_ggor_2070, retro_ggor_379,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Macaca mulatta	ENSMMUG00000012634	2 retrocopies	retro_mmul_1913, retro_mmul_483,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Otolemur garnettii	ENSOGAG00000012517	1 retrocopy	retro_ogar_2772,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pan troglodytes	ENSPTRG00000005840	3 retrocopies	retro_ptro_2022 , retro_ptro_288, retro_ptro_2932,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,