RetrogeneDB ID: retro_ggor_2570

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:16699829..16701654(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN2L
• Ensembl ID: ENSGGOG00000014112
• Aliases: None
• Description: None

Sequence

>retro_ggor_2570
GCTTCCTGCGCAGCTCCACCGGGGCCTCCTGCAGCCTCCTCCGCCTGCCTGGGGCCTTCGGCTGCGGGGAGCGGGCTCCG
CTGGGGAGCCGAAAGCATCTTGACAACGCAGCCGCCACCGCAGCAGCAGCACCAGGAGAGGCCGGGGGCCGCTGCCATCG
GCAGCGCCAGGGGACAGAGCACAGGAAAGGGACCTCCGCAGTCACCTGTGTTCGAAGGCGTCTACAACAATTCCAGAATG
CGGCACTTCCTTACAGCTGTTGTGGGCTCCGCTTGTGATGTAAAGGTGAAAAATGGCAGCACCTATGAGGGTATCTTCAA
GACGCTGAGCTCAAATTTTGAACTAGCAGAGGATATTGTACACCAGAAAGCATCTGAGCCAGCAGGTGGCCCTCGTCGGG
AGGACACTGTAGACACCATGGTGTTTAAGCCAAGTGATGTCATGCTTGTTCACTTCCGAAATGCTGACTTCAGCTGCGCT
ACTAAAGACAAGTTCACCGATTCAGCCATCGCCATGAACTCGAAGGGAATGGGGAACACAAAGAGAAGGTGCTTCAGCGC
TGGGAGCGGGTTGACAGCAACAGCGACAACTACGACCTCGAGTCCAACATGTCCAATGGATGGGACCCCAACGAAATGTT
CAAGTTCAATGAGGAGAACTACGGTGTGAAGACCACCTATGACAGCAGTCTTTCTGCTTATACGGTGCCCTTAGAAAAGG
ACAACTCGAAAGTTTCAGCTGAGAGCTGCGTGCGGCCCAGTTGGCTCCAGAGATTGAATCAAGCCCCCAGTACCGCCTGC
GGATCGCCATGCAGAGCGACGATGGGCGCACTGAAGAGGAGAAGCACACGGCGGTCCAGCGGCAGGGGTCGGGGCGGGAG
AGCCCCAGCTTGGCATCCAGGAAGGGGAAGTGTATCATCCCTCTGCCTCAACGAGTCCAGGAAGGTCCCCGGGGAGGAGT
TTGACGCAGCAGCCCTCTGGGCAGTCAGCCTGGCCTTAGCAATTTGTCACCTCGTGGCCCTCACCATCTGGACAATAGCA
ATCCTGGCCCAGGTTCTGAGGCCCGTGGTATCAATGAAGGCCCTTCCCACATGTCCCCAAAGGCACAGAGGCCTCTGAGA
GGTGCCAAGACTCTGTCTTCGCCCAATAATAGGCCTTCCGGAGAAACTTCTGTTCCTCCTCCTGCAGTGGGCCGGATGTA
TCCCCCGAGTTCTCCCAAGTCTGCTGCCCCTGCCCCAATCTCACCTTCCTGTCCTAAGCTTCCCATTGGCTTGGCAGTGC
CAACCTCTTCAGCCTCCATCCCTGTGACCTCATCAGTCTCAGATCCTGGAATGGGCTACATTTCCTCAGCTTCTCCAAAG
ATCTCCCTGGCCCCCACAGATGTAAAAGAACTCTCTACCAAGGAACCTGGGAGAACCCTGGAGCCCCAGTAGCTGGCTCA
GATAGCTGAGAAAGTCCCTGGTCTTCAGAATGAACAGAAACTATTCCAACTGGAAGAACTGAGAAAGTGTGGGGCCCAGT
TTAAGCTTCAGCCCGGTAGTTCCCCTGAGAACAGCCTGGATCCTTTTCCTCCCTGGACCTTAAAGGAGGAGGCCAAAGGA
AAGGAGAAGGAGGATGTTGGTCTGTTGACTTCAAAACCCATGGGGTCCCCCGTCTCCTCCAAGACAGAGTCTGTATCGGA
TAAGGAGGACAAACCACCCCTGGCACCAGCAGGAGGCACTGAGGGGCCAGAGCCGCCCCCACCACCTTGCCCAAGCCAAA
CTGGCAGCCTCCCCTTTGGCCTCATCAAAGGAGAGGACAAGGATGAGGGCCCTATTGCTGAACAA

Alignment

ORF - retro_ggor_2570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.83 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATSAAPPGPPAAASPCLGPVAAAGSGLRRGAEGILAPQPPPPQQHQERPGAAAFGGNRGQSTGKGPPQSP
          A..AAPPGPPAA.S.CLGP..AAGSGLR.GAE.IL..QPPP.QQHQERPGAAA.G..RGQSTGKGPPQSP
Retrocopy ASCAAPPGPPAASSACLGP-SAAGSGLRWGAESILTTQPPPQQQHQERPGAAAIGSARGQSTGKGPPQSP

Parental  VFEGVYNNSRMLHFLTAVVGSTCDVKVKNGTTYEGIFKTLSSKFELAVDAVHRKASEPAGGPRREDIVDT
          VFEGVYNNSRM.HFLTAVVGS.CDVKVKNG.TYEGIFKTLSS.FELA.D.VH.KASEPAGGPRRED.VDT
Retrocopy VFEGVYNNSRMRHFLTAVVGSACDVKVKNGSTYEGIFKTLSSNFELAEDIVHQKASEPAGGPRREDTVDT

Parental  MVFKPSDVMLVHFRNVDFNYATKDKFTDSAIAMNSKV-NGEHKEKVLQRWEGGDSNSDDYDLESDMSNGW
          MVFKPSDVMLVHFRN.DF..ATKDKFTDSAIAMNSK..NGEHKEKVLQRWE..DSNSD.YDLES.MSNGW
Retrocopy MVFKPSDVMLVHFRNADFSCATKDKFTDSAIAMNSKG<NGEHKEKVLQRWERVDSNSDNYDLESNMSNGW

Parental  DPNEMFKFNEENYGVKTTYDSSLSSYTVPLE-KDNSEEFRQRELRAAQLAREIESSPQYRLRIAMENDDG
          DPNEMFKFNEENYGVKTTYDSSLS.YTVPLE.K...E.F...ELRAAQLA.EIESSPQYRLRIAM..DDG
Retrocopy DPNEMFKFNEENYGVKTTYDSSLSAYTVPLE<KGQLESF-S*ELRAAQLAPEIESSPQYRLRIAMQSDDG

Parental  RTEEEKHSAVQRQGSGRESPSLASREGK-YIPLPQRVREGPRGGVRCSSSRGGRPGLSSLPPRGPHHLDN
          RTEEEKH.AVQRQGSGRESPSLASR.GK..IPLPQRV.EGPRGGV..SS..G..PGLS.L.PRGPHHLDN
Retrocopy RTEEEKHTAVQRQGSGRESPSLASRKGKCIIPLPQRVQEGPRGGV*RSSPLGSQPGLSNLSPRGPHHLDN

Parental  SSPGPGSEARGINGGPSRMSPKAQRPLRGAKTLSSPSNRPSGETSVPPPPAVGRMYPPRSPKSAAPAPIS
          S.PGPGSEARGIN.GPS.MSPKAQRPLRGAKTLSSP.NRPSGETSVPPP.AVGRMYPP.SPKSAAPAPIS
Retrocopy SNPGPGSEARGINEGPSHMSPKAQRPLRGAKTLSSPNNRPSGETSVPPP-AVGRMYPPSSPKSAAPAPIS

Parental  ASCPEPPIGSAVPTSSASIPVTSSVSDPGVGSISPASPKISLAPTDVKELSTKESGRTLEPQELARIAGK
          .SCP..PIG.AVPTSSASIPVTSSVSDPG.G.IS.ASPKISLAPTDVKELSTKE.GRTLEPQ.LA.IA.K
Retrocopy PSCPKLPIGLAVPTSSASIPVTSSVSDPGMGYISSASPKISLAPTDVKELSTKEPGRTLEPQ*LAQIAEK

Parental  VPGLQNEQKRFQLEELRKFGAQFKLQPSSSPENSLDPFPPRILKEEPKGKEKEVDGLLTSEPMGSPVSSK
          VPGLQNEQK.FQLEELRK.GAQFKLQP.SSPENSLDPFPP..LKEE.KGKEKE..GLLTS.PMGSPVSSK
Retrocopy VPGLQNEQKLFQLEELRKCGAQFKLQPGSSPENSLDPFPPWTLKEEAKGKEKEDVGLLTSKPMGSPVSSK

Parental  TESVSDKEDKPPLAPSGGTEGPEQPPPPCPSQTGSPPVGLIKGEDKDEGPVAEQ
          TESVSDKEDKPPLAP.GGTEGPE.PPPPCPSQTGS.P.GLIKGEDKDEGP.AEQ
Retrocopy TESVSDKEDKPPLAPAGGTEGPEPPPPPCPSQTGSLPFGLIKGEDKDEGPIAEQ

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	0.24 RPM	105.93 RPM
SRP007412_cerebellum	0.16 RPM	145.06 RPM
SRP007412_heart	0.06 RPM	31.93 RPM
SRP007412_kidney	0.04 RPM	54.38 RPM
SRP007412_liver	0.03 RPM	38.64 RPM
SRP007412_testis	1.45 RPM	276.51 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_2570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2570 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3820
Pan troglodytes	retro_ptro_2598
Macaca mulatta	retro_mmul_1631

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000168488	1 retrocopy	retro_hsap_3820,
Gorilla gorilla	ENSGGOG00000014112	1 retrocopy	retro_ggor_2570 ,
Macaca mulatta	ENSMMUG00000003298	1 retrocopy	retro_mmul_1631,
Pan troglodytes	ENSPTRG00000007938	1 retrocopy	retro_ptro_2598,