RetrogeneDB ID: retro_ggor_3055

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:113388132..113389624(-)
• Located in intron of: None

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_3055
GTGCCGAAGGTAGAGGAGCTTTACCGCAATTATGGCATCCTGGCCGATGCCATGGAGCAAGTGGTCCAACATAAAAATGC
CTATGAAGTGATACCGGGTGGTGTGAAAGGTGGTACTAAGGAAAAACGATTAGTAGCCCAATTTATTCCGAAATTCTTTA
AGCAGTTTCCAGAATTGGCTGATTCTGCTATCAATGCACTGTTAGACCTCTGTGAGGATGAAGATGTATCTATTCGACGT
CAAGCAATTAAAGAACTGCCTCAATTTGCCACTGGAGAAAATCTTCCTCGAGTGGCAGATATACTAACACAAGTTTTGCA
GACAGATGACTCTGCAGAATTTAACCTAGTCAACAATGCCCTGTTAAGTATATTTTAAATGGATGCAAAAGGAACTTTAG
GTGGGTTGTTCAGCCAAATACTTCAAGGAGAGGACATTGTTAGAGAACGAGCAATTAAATTCCTTTCTACAGAACTTAAG
ACTTTACCAGATGAAGTCTTAACAAAGGAAGTGAAAGAGCTTATACTAACTGAATCCAAAAAGGTCCTAGAAGATGTGAC
TGGTTAAGAATTTGTTCTATTATGAAGATACTGTCTGGGTTAAAAAGCTTACAGTGAGTGGAAGATAGCAACTTGTAGAG
TTGGTGGCTGAACAGGCCAACCTAGAACAGACCTTCAATCCCTCGGATCCTGACTGTGTGTACAGGCTCTTACAGTACAC
TCGGCAAGCAGTACCCCTCTTCTCTAGAATTATCCATTCCACAAGGTTTGTGACATATTTCTGTGAGCAGGTTCTCCCTA
ACCTCAGTACCTTGACTACCCCAGTGGAAGGTCTTGATATACAGTTGGAGGTATTGAAATTGTTGGCTGAGATGAGTTCA
TTTTGTGCTGACATGGAAAAACTAGAAACAAATTTAAGAAAACTATTTGATAAGTTATAGGAGTACATGCCGCTCCCTCC
AGAAGAAGCAGAAAATGGAGAGAATGCTGGTAATGAAGAACCCAAGCTACAGTTCAGTTATGTGGAATGTTTGTTGTACA
GTTTTCACTAGTTGGGCCGAAAACATCCAGATTTCTTAACAGCCAAACTGAATGCAGAAAAGCTCAAAGATTTCAAAATC
AGGCTGCAGTACTTTGCACGGGGCCTGCAAATTTATATCAGACAACTTCGCTTAGCTCTCCAGGGTAAAACGGGTGAGGC
CTTAAAAAGAGAAGAGAACGAGATTAAAGTCGTTGCATTGAAAATAACAAACAATATCAATGCTTTAATCAAGGATCTCT
TCCACATTCCTCCTTCTTATAAGAGCACAGTAACACTATCCTGGAAACCTGTACAAAAGGTTGAGATTGGGCAAAAGAGA
GCCAGTGAAGATACAACCTCAGGTTCACCACCCAAGAAATCTTCAGCAGGACCAAAAAGAGATGCCAGGCAGATTTATAA
CCCTCCCAGTGGGAAATATAGCAGCAATTTGAGCAACTTTAATTATGAGAGG

Alignment

ORF - retro_ggor_3055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 95.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDL
          .P.VEELYRNYGILADA.EQV.QHK.AY.VI..GVKGGTKEKRL.AQFIPKFFK.FPELADSAINA.LDL
Retrocopy VPKVEELYRNYGILADAMEQVVQHKNAYEVIPGGVKGGTKEKRLVAQFIPKFFKQFPELADSAINALLDL

Parental  CEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQI
          CEDEDVSIRRQAIKELPQFATGENLPRVADILTQ.LQTDDSAEFNLVNNALLSIF.MDAKGTLGGLFSQI
Retrocopy CEDEDVSIRRQAIKELPQFATGENLPRVADILTQVLQTDDSAEFNLVNNALLSIF*MDAKGTLGGLFSQI

Parental  LQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLF-MKILSGL-KSLQTVS
          LQGEDIVRERAIKFLST.LKTLPDEVLTKEV.ELILTESKKVLEDVTG.EFVL..MKILSGL.K.L.TVS
Retrocopy LQGEDIVRERAIKFLSTELKTLPDEVLTKEVKELILTESKKVLEDVTG*EFVLL<MKILSGL<KKL-TVS

Parental  GRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVE
          GR.QLVELVAEQA.LEQTFNPSDPDCV.RLLQ.TRQAVPLFS...HSTRFVTYFCEQVLPNL.TLTTPVE
Retrocopy GR*QLVELVAEQANLEQTFNPSDPDCVYRLLQYTRQAVPLFSRIIHSTRFVTYFCEQVLPNLSTLTTPVE

Parental  GLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLY
          GLDIQLEVLKLLAEMSSFC.DMEKLETNLRKLFDKL.EYMPLPPEEAENGENAGNEEPKLQFSYVECLLY
Retrocopy GLDIQLEVLKLLAEMSSFCADMEKLETNLRKLFDKL*EYMPLPPEEAENGENAGNEEPKLQFSYVECLLY

Parental  SFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFAKGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKIT
          SFH.LGRK.PDFLTAKLNAEKLKDFKIRLQYFA.GLQ.YIRQLRLALQGKTGEALK.EEN.IKVVALKIT
Retrocopy SFH*LGRKHPDFLTAKLNAEKLKDFKIRLQYFARGLQIYIRQLRLALQGKTGEALKREENEIKVVALKIT

Parental  NNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPSGKY
          NNIN.LIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPSGKY
Retrocopy NNINALIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPSGKY

Parental  SSNLGNFNYEQ
          SSNL.NFNYE.
Retrocopy SSNLSNFNYER

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	1.10 RPM	25.99 RPM
SRP007412_cerebellum	1.30 RPM	23.40 RPM
SRP007412_heart	0.16 RPM	3.88 RPM
SRP007412_kidney	1.59 RPM	19.91 RPM
SRP007412_liver	0.66 RPM	9.79 RPM
SRP007412_testis	1.66 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_3055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3055 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4893
Pan troglodytes	retro_ptro_3261
Pongo abelii	retro_pabe_3805

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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,