RetrogeneDB ID: retro_ggor_1784

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:65980158..65981345(-)
• Located in intron of: ENSGGOG00000034968

Retrocopy information

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

Parental gene information

• Parental gene symbol: API5
• Ensembl ID: ENSGGOG00000002358
• Aliases: None
• Description: None

Sequence

>retro_ggor_1784
AATGCCCTGTTGAGTATATTTAACATGGATGAAAAAGGGACTTTAGGTTCATTGTTCAGCCAAATACTTCAAGGAGAGGA
CACTGTTAGAGAACGAGCAATTAAATTCCTTTCTACAAAACTTAAGACTTTACCAGATGAAGTATTAACAAAGGAAGTGG
AAGAGCTTATACTAACTGAATCCAAACACGTCCTAGAAGATGTGACTCATGAAGAATTTGTTCTATTCATGAATTACTGT
CTGGGTTAAAAAGCTTACAGACAGTAAGTGGAAGACAGCAACTTGTAAAGTTGGTGGCTGAACAGGCTGACCTAGAACAG
ACCTTCAATCCCTCAGATCCTGAGTGTGTGGGCAGGCTCTTACAGTGCACTCAGCAGGCAGTACCCTTCTTCTCTAAAAC
TGTCCATTCCACAAGGTCTGTGACATATTTCTGTGAGCAGGTTCTCCCTAACCTTGGTATCTTGACTACCACAGTGGAAG
GTCTTGACATACAGTTGGAGGTATTGAAATTGTTGGTGGAGATGAGTTCATTTTGTGGTGACGTGGAAAAACTAGAAACA
AATTTAGGGAAACTATTTGATAAGTTATTGGAATACATGCCCCTCCCTCCAGAAGAAGCAGAAAATGGAGGGAATGCTGG
TGATGAAGAACCCAAACTACAGTTCAGTTATGTGGAATGTTTGTTGTACAGTTTTCACCAGTTGGGCCAAAAACTTCCAG
ATTTCTTAACAGCCAAACTGAATGCAGAAAAACTCAAAGATTTCAAAATCAGGCTGCAATACTTTGCATGAGGCCTGCAA
GTTTATATCAGACAACTTCGCTTAGCTCTCCAGGGTGAAACGGGTGAGAACAGAAGAGAACAGAAAACAGAAGAGAACAA
AATTAAAGTTGTTGCATTGAAAGCAACAAACAATATCAATGTTTTAATCAAGGATCTCTTCCACATTCCTCCTTCTTGTA
AGAGCACAGTAACACTATCCTGGAAACCTGTACAAAAGGTTGAGATTGGGCAAAAGAGAGCCAGTGAATATACAACTTCA
GGTTCACCACCCCAGAAATCTTCAGCAGGACAAAAAAGAGATGCCAGGCAGATTTATAATCCTCCCAGTGAGAAATATAG
CAGCAATTTGGGCAACTTTAATTATGAGAGGAGCCTTCAGGGAAAGTAGAGGGGGCCGAGGTTGGGG

Alignment

ORF - retro_ggor_1784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.66 %
• Parental protein coverage: 74.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTG
          NALLSIF.MD.KGTLG.LFSQILQGED.VRERAIKFLSTKLKTLPDEVLTKEVEELILTESK.VLEDVT.
Retrocopy NALLSIFNMDEKGTLGSLFSQILQGEDTVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKHVLEDVTH

Parental  EEFVLFM-KILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTR
          EEFVLFM...LSGLKSLQTVSGRQQLV.LVAEQADLEQTFNPSDP.CV.RLLQCT.QAVP.FSK.VHSTR
Retrocopy EEFVLFM<ELLSGLKSLQTVSGRQQLVKLVAEQADLEQTFNPSDPECVGRLLQCTQQAVPFFSKTVHSTR

Parental  FVTYFCEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAEN
          .VTYFCEQVLPNLG.LTT.VEGLDIQLEVLKLL.EMSSFCGD.EKLETNL.KLFDKLLEYMPLPPEEAEN
Retrocopy SVTYFCEQVLPNLGILTTTVEGLDIQLEVLKLLVEMSSFCGDVEKLETNLGKLFDKLLEYMPLPPEEAEN

Parental  GENAGNEEPKLQFSYVECLLYSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFAKGLQVYIRQLRLALQG
          G.NAG.EEPKLQFSYVECLLYSFHQLG.KLPDFLTAKLNAEKLKDFKIRLQYFA.GLQVYIRQLRLALQG
Retrocopy GGNAGDEEPKLQFSYVECLLYSFHQLGQKLPDFLTAKLNAEKLKDFKIRLQYFA*GLQVYIRQLRLALQG

Parental  KTGE---ALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGS
          .TGE.....KTEENKIKVVALK.TNNINVLIKDLFHIPPS.KSTVTLSWKPVQKVEIGQKRASE.TTSGS
Retrocopy ETGENRREQKTEENKIKVVALKATNNINVLIKDLFHIPPSCKSTVTLSWKPVQKVEIGQKRASEYTTSGS

Parental  PPKKSSAGPKRDARQIYNPPSGKYSSNLGNFNYEQ--RGAFRGSRGG
          PP.KSSAG.KRDARQIYNPPS.KYSSNLGNFNYE....G..RG.R.G
Retrocopy PPQKSSAGQKRDARQIYNPPSEKYSSNLGNFNYERSLQGK*RGPRLG

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	25.99 RPM
SRP007412_cerebellum	0.00 RPM	23.40 RPM
SRP007412_heart	0.00 RPM	3.88 RPM
SRP007412_kidney	0.04 RPM	19.91 RPM
SRP007412_liver	0.00 RPM	9.79 RPM
SRP007412_testis	0.10 RPM	32.94 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_1784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1784 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2350
Pan troglodytes	retro_ptro_1720
Macaca mulatta	retro_mmul_947

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166181	2 retrocopies	retro_hsap_2350, retro_hsap_4893,
Gorilla gorilla	ENSGGOG00000002358	2 retrocopies	retro_ggor_1784 , retro_ggor_3055,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Nomascus leucogenys	ENSNLEG00000017956	1 retrocopy	retro_nleu_352,
Pan troglodytes	ENSPTRG00000003516	2 retrocopies	retro_ptro_1720, retro_ptro_3261,