RetrogeneDB ID: retro_acar_108

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:94514073..94515178(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP14
• Ensembl ID: ENSACAG00000008213
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G1KHK9]

Sequence

>retro_acar_108
TTACACTCTGTGCCAGAACTGAAAGAAGCTCTTAAGAGGTATGCTGGTGCATTAAGAGCTTCAGGGGAAATGGCCTCTGA
TCAGTATATTACTCCAGCTCTTAAGAGATTTATTTTATTCCATTGATAAAACCTCCTCTAGTATCATCATTCTCCTCCAG
TTTTAACACATGGCCTTTCCTCAGTTCACTGAGAAAGACGATCAAGGCCAGTATCTTCAACAGGGTGGTGACGAATGTTG
GGTACAGATGATGTGAGAACTGCAGCAGAAGATAGAAGGGATAGAAGGCGATTCAGTTGTGGAAACTGACCCTGGAGCTT
CATGAGCAGCTGGCTGCACCTCCTCAGAAAATGAGCTTAATTGATCAGTTGTTCAGTATTGAATTTGAAACTACCATGAA
ATGTATAGAAGCAGAAGAGGAGGATATCACAAAAGGAAGAGATAATCAATTCCAACTTAGTTACTTAATCATTCAAGAAG
TTAAATATCTTTTCACTGGTCTTAAACTGCGCCTTCAAGAAGAAATCATCAAACTGTCTCCAACCTTGCAAAAAAAATGC
ATTTCACATTTTTTTTCCAAAATAAGTCACCTGCCTGCTTACCTGACTATTCAGATGGCTTTTACAAAGAGAGAGAATCT
GTAAATGCAAAAGTTCCCAAGGATGTTAAGTTTTTTCTTATGTTGGATGTATATGATTTATGTAGATCAGAACTTCAAGA
GAACATGGATGCCTACCAATCAAAATTCAAGGACTTGAAAGACAAGAAAGTGAAACAAACAAAGCATTCTCGTAAAGGTG
ATGTTGCACAGAAAAAAGTTAAACATGAAGCATTTTCCTTTCCTGATGATATTGCCTCCAATATCTGTGGTTATTATGAA
CTGCAGGCTGTGTTAACACATCAAGGAAAATTTAGTTCTTCTGGACACTATGTATCTTTGGTTAAAAGAAAAGAAGATGA
ATTGATCAAATTTCATGATGACAAAGTCAGCACTGTTACACCAGAAGAAAACTTGAGGTTATGTGGGGGTGGAGACTGGC
ATATAGCTTACATCCTATTTTATGGGCCACACAGAATTAAAGTAATAAAAGATGAAGATGAACAA

Alignment

ORF - retro_acar_108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.39 %
• Parental protein coverage: 75.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IRSVPELKEALKRYAGALRASGEMASAQYITAAL-RDLFDSMDKTSSSIPPIILLQFLHMAFPQFAEKGD
          ..SVPELKEALKRYAGALRASGEMAS.QYIT.AL.RDLF.S.DKTSSSI..IILLQF.HMAFPQF.EK.D
Retrocopy LHSVPELKEALKRYAGALRASGEMASDQYITPAL>RDLFYSIDKTSSSI--IILLQF*HMAFPQFTEKDD

Parental  QGQYLQQDANECWVQMMRVLQQKLEGIEGDTVMETDPGASGAA-AAPPKKKSLIDQFFSIEFETTMKCTE
          QGQYLQQ...ECWVQMM..LQQK.EGIEGD.V.ETDPGAS.AA.AAPP.K.SLIDQ.FSIEFETTMKC.E
Retrocopy QGQYLQQGGDECWVQMM*ELQQKIEGIEGDSVVETDPGAS*AA>AAPPQKMSLIDQLFSIEFETTMKCIE

Parental  AEEEEVTKGRENQLQLSCFINQEVKYLFTGLKLRLQEEITKLSPTLQRNALYIKSSKISRLPAYLTIQMV
          AEEE..TKGR.NQ.QLS..I.QEVKYLFTGLKLRLQEEI.KLSPTLQ........SKIS.LPAYLTIQM.
Retrocopy AEEEDITKGRDNQFQLSYLIIQEVKYLFTGLKLRLQEEIIKLSPTLQKKCISHFFSKISHLPAYLTIQMA

Parental  RFFYKEK-ESVNAKVLKDVKFPLMLDVYELCTPELQESMVPYRSKFKDLEDKKVNQQTKNSSKGDGAQKE
          ..F.K...ESVNAKV.KDVKF.LMLDVY.LC..ELQE.M..Y.SKFKDL.DKKV..QTK.S.KGD.AQK.
Retrocopy --FTKRE<ESVNAKVPKDVKFFLMLDVYDLCRSELQENMDAYQSKFKDLKDKKV-KQTKHSRKGDVAQKK

Parental  VKYEAFSFPDDIGSNNCGYYELQAVLTHQGRSSSSGHYVSWVKRKEDEWIKFDDDKVSTVTPEDILRLSG
          VK.EAFSFPDDI.SN.CGYYELQAVLTHQG..SSSGHYVS.VKRKEDE.IKF.DDKVSTVTPE..LRL.G
Retrocopy VKHEAFSFPDDIASNICGYYELQAVLTHQGKFSSSGHYVSLVKRKEDELIKFHDDKVSTVTPEENLRLCG

Parental  GGDWHIAYVLLYGPRRIEVMEEEAEQ
          GGDWHIAY.L.YGP.RI.V...E.EQ
Retrocopy GGDWHIAYILFYGPHRIKVIKDEDEQ

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
SRP009831_adrenal	0.00 RPM	49.27 RPM
SRP009831_brain	0.00 RPM	44.88 RPM
SRP009831_dewlap	0.00 RPM	134.79 RPM
SRP009831_embryo	0.00 RPM	145.35 RPM
SRP009831_heart	0.00 RPM	50.33 RPM
SRP009831_liver	0.00 RPM	31.29 RPM
SRP009831_lung	0.00 RPM	33.90 RPM
SRP009831_ovary	0.00 RPM	143.43 RPM
SRP009831_skeletal_muscle	0.00 RPM	69.20 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_108 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_108 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008213	1 retrocopy	retro_acar_108 ,
Choloepus hoffmanni	ENSCHOG00000010588	4 retrocopies	retro_chof_1736, retro_chof_2406, retro_chof_2529, retro_chof_2603,
Echinops telfairi	ENSETEG00000004949	1 retrocopy	retro_etel_966,