RetrogeneDB ID: retro_ggor_2070

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:157690879..157691559(+)
• Located in intron of: ENSGGOG00000000619

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSGGOG00000006657
• Aliases: None
• Description: None

Sequence

>retro_ggor_2070
CAGATTCCTGAATATTTGTCACAGCAATGAGCTGAAGCCCCTGGAAGAGGTGAAGTTAGGAAACTGTGGATTGCCAAGAC
TCAAGGAAGAACTGAGGTGTCATTTACTTTGAATGAAGATCTTGCAAATATTCATGATATTGGCCGAAAAGCAGCTTCAG
TCAGTACTCATAAAGAACATCCATTTGTCTTGCAAAATGTTGGAGGCCATATATGAACAATATTTACTGAGAGCTCATCA
GATAAGCTGTCTTTGGAAGGAATAGTGGTACAAAGAACTGAATGCCAACAGACTGCCAGTGAAAAGTACATGAGATTAAA
AAGATTGCAAATAGAGGAATCTTCCAAACCTGTAAGGCTATCGCAACAACTGGACAAAGTTGTAACAGCCAGTTTTGAAA
CTGTTGCTAATCAATACAATACTGAATGTGAAAGGAAAGAGAAAGCAGATGGAAAATAAGCTCCAGCTAATAAACAACAC
GTTTCAGACATGCTATTTTCAGCCTTTAGAAATATCAATATTATCATCTTAAGGACTTGGTGGACATCACAAAACAACCT
GTGGTATACCTGAGGGAACTCTTAAAAGAAATTGGTCTTCAGAATGTAAAAGAGATCCACAAAAACACGTGGGAGCTGAA
ACCAGAGTACAGACATCACCAAGGAGAAGAAATGAGTGAT

Alignment

ORF - retro_ggor_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.48 %
• Parental protein coverage: 91.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVPKYLSQQWAKASGRGEVGKLRIAKTQGRTEVSFTLNEDLANIHDIGGKPASVSAPREHPFVLQSVGGQ
          ..P.YLSQQ.A.A.GRGEV.KL.IAKTQGRTEVSFTLNEDLANIHDIG.K.ASVS...EHPFVLQ.VGG.
Retrocopy QIPEYLSQQ*AEAPGRGEVRKLWIAKTQGRTEVSFTLNEDLANIHDIGRKAASVSTHKEHPFVLQNVGGH

Parental  TLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANHQY
          ..T.FTESSSDKLSLEGIVVQR.EC...ASE.YMRLKRLQIEESSKPVRLSQQLDKVVT.....VAN.QY
Retrocopy I*TIFTESSSDKLSLEGIVVQRTECQQTASEKYMRLKRLQIEESSKPVRLSQQLDKVVTASFETVAN-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	0.05 RPM	7.10 RPM
SRP007412_cerebellum	0.00 RPM	6.38 RPM
SRP007412_heart	0.09 RPM	2.81 RPM
SRP007412_kidney	0.00 RPM	10.30 RPM
SRP007412_liver	0.03 RPM	7.52 RPM
SRP007412_testis	0.00 RPM	23.62 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2070 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2990
Pan troglodytes	retro_ptro_2022
Macaca mulatta	retro_mmul_1913

---

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,