RetrogeneDB ID: retro_acar_178

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343320.1:99425..100360(-)
• Located in intron of: ENSACAG00000017419

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB13
• Ensembl ID: ENSACAG00000006460
• Aliases: None
• Description: None

Sequence

>retro_acar_178
ATGGGGCAGGACTACTACGCCGTGCTGGAACTCACCCAAAGCCCCAAGGACGCCGACATCAAGAAGGCTTATTGGAAACT
AGCATTGAAGTACCCTTATAAGAATGATGCACCTTGGGCTCAGGAGAATTTCAAGCAAATTGCAGAAGTCTATGATGCCT
TGAGCAACCCAGTGAAGAAAGGAGTCTATGATAAATTGGCCTTAAAGGAGGGATTTTTCTGGAGTTTGGGATTAACACTC
CCTGGATAGAAGGCTATGTATTCCATGGAAGGCCAGAGAATGTCTTGCACGATTTCTTTGGAGGAGACAACCCTTTTGCT
GAACTCTACATTGCTGAAGGGGCGGAAGTGAAGATGGCCTTTGGAGGCCTGCAAGGGCAGTGAGTGAAGAAGCAAGACCC
TCCCAGTGAACGAGAACTTTCTCTCTCCCTGGAAGACCTATTCTATGGGTGTACCAAAAAAATCAAGATTTCACGCAGGA
TGATGAATGAAGATGGCCACGTGTCCACCATTAAAGATAAGATCCTCACCATTGATGTCTAGCCAAGGTGGAAGCAAGGG
ACCAGGATCACTTTTCCAGAAGAGGGGGACCAGGGCCCCAATACCATCCCAGCAGACATAATCTTCATTGTCAAAGAGAA
GATCCACCCCCAGTTCAAACAAGACGAGGACAACCTGATTTATGTGATCAAGATCACACTGGGAAAGGCTCTGATTGGGT
GCACCATTGAAATAAGTATGCTGGATGAGCGCCTTCTCAACATCCCCATCAATGACATTGTCCACCCCAAATATTTCAAG
ATTGTGCCGGGAGAAGGGATGCTTCTGTCCCAAGACCCCACCTGCAAAGGGGACCTCTTCATGTACTTTGACATCGTCTT
CCCCGCAAAGCTGACCCCCGCCAAGAAGGACCTCCTGCGGGAACCCCTCCTGACA

Alignment

ORF - retro_acar_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGQDYYAMLELTRSAKDADIKKAYRKLALKYHPYKNDAPWAAEKFKQIAEAYDVLSDPLKKGVYDKFAEE
          MGQDYYA.LELT.S.KDADIKKAY.KLALKY.PYKNDAPWA.E.FKQIAE.YD.LS.P.KKGVYDK.A..
Retrocopy MGQDYYAVLELTQSPKDADIKKAYWKLALKY-PYKNDAPWAQENFKQIAEVYDALSNPVKKGVYDKLA--

Parental  GLKGG-IPLEFGIDTPWTEGYVFHGRPEKVFRDFFGGDNPFAEFYTAEGAEVNMAFGGLRGRGVKKQDPP
          .LK.G.I.LEFGI.TPW.EGYVFHGRPE.V..DFFGGDNPFAE.Y.AEGAEV.MAFGGL.G..VKKQDPP
Retrocopy -LKEG<IFLEFGINTPWIEGYVFHGRPENVLHDFFGGDNPFAELYIAEGAEVKMAFGGLQGQ*VKKQDPP

Parental  IERDLYLSLEDLFYGCTKKIKISRRVMNEDGHASTIKDKILTIDVQPGWKQGTRITFPEEGDQGPNIIPA
          .ER.L.LSLEDLFYGCTKKIKISRR.MNEDGH.STIKDKILTIDV.P.WKQGTRITFPEEGDQGPN.IPA
Retrocopy SERELSLSLEDLFYGCTKKIKISRRMMNEDGHVSTIKDKILTIDV*PRWKQGTRITFPEEGDQGPNTIPA

Parental  DIIFIVKEKIHPRFKRDEDNLIYVAKIPLGKALIGCTIDVSTLDERLLNIPINDIVHPKYFKVVPGEGMP
          DIIFIVKEKIHP.FK.DEDNLIYV.KI.LGKALIGCTI..S.LDERLLNIPINDIVHPKYFK.VPGEGM.
Retrocopy DIIFIVKEKIHPQFKQDEDNLIYVIKITLGKALIGCTIEISMLDERLLNIPINDIVHPKYFKIVPGEGML

Parental  LSQNPTCKGDLFMYFDIVFPARLTPAKKDLLREALLT
          LSQ.PTCKGDLFMYFDIVFPA.LTPAKKDLLRE.LLT
Retrocopy LSQDPTCKGDLFMYFDIVFPAKLTPAKKDLLREPLLT

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	0.53 RPM
SRP009831_brain	0.00 RPM	4.40 RPM
SRP009831_dewlap	0.00 RPM	3.21 RPM
SRP009831_embryo	0.00 RPM	7.47 RPM
SRP009831_heart	0.00 RPM	1.40 RPM
SRP009831_liver	0.00 RPM	1.10 RPM
SRP009831_lung	0.00 RPM	10.93 RPM
SRP009831_ovary	0.00 RPM	6.64 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.25 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_178 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_178 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006460	2 retrocopies	retro_acar_166, retro_acar_178 ,
Bos taurus	ENSBTAG00000003682	1 retrocopy	retro_btau_1139,