RetrogeneDB ID: retro_dnov_1275

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17437:47004..47606(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSDNOG00000015166
• Aliases: None
• Description: cyclin G1 [Source:HGNC Symbol;Acc:1592]

Sequence

>retro_dnov_1275
GTCAAGGTACAGCCCAAGATCTTGGCTGTGTTGGATTGAGCTGTTTTTATTTGGCTGTAAAATTGATTGAAGAGGAAAGG
AATGTCCCACTGGCAACTGACTTGACCCATATAAACCAGTATAGGTTCATGGTTTCAGACTTGATAAGGATGGAAAAGAT
TATATTGGAAAGGTGTGTTGGAAAGTCAAAGCAACAACTGCCTTTAAATTTCTGCAAATCCATTATTCACTCATTCATGA
GAACATTCATGTGAAAGGAGAAACAGGCTTAATTCTGAAAGAAGAGAAACTCAATTTAAGGCATGCCACTGCAGAATGAT
ATTTTCTAAAGCTAAGTCTTCTGTGTCGACATTCTCTATCACTTCATTAGACATCCAAGCAAAGAAGTGTATAGAATTAA
CGGAAGTAGAATGTCTTCAGAAACAGTCCAAGACAAATGGCAGAGATCTGAACATCTGGTAAGAGCTCATATCCCAGTGT
TTAAATGAATAATCATTAACAAGTGTTCCAAACCAAATGTTCAGAGATCAAGGATTGTTTCTGGGAGTACTACATGGAAA
CTAAAGTATAGCTACCACAGAATCACACATCTTCCAACAATT

Alignment

ORF - retro_dnov_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 70.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKVQPK-HLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLE-KVCWKVKATTA
          .KVQPK..LGCVGLSCFYLAVK.IEEERNVPLATDL..I.QYRF.VSDL.RMEKI.LE.KVCWKVKATTA
Retrocopy VKVQPK<DLGCVGLSCFYLAVKLIEEERNVPLATDLTHINQYRFMVSDLIRMEKIILE<KVCWKVKATTA

Parental  FQFLQLYYSLIHENM-PCERKNSLNFERLEAQLKACHCRIIFSKAKPSVLALSIIALEIQAQKCIELTEG
          F.FLQ..YSLIHEN...CER.N.LN.ER.E.Q.KACHCR.IFSKAK.SV...SI..L.IQA.KCIELTE.
Retrocopy FKFLQIHYSLIHENI<SCERRNRLNSERRETQFKACHCRMIFSKAKSSVSTFSITSLDIQAKKCIELTE-

Parental  VECLQKHSKINGRDLIFWQELVSKCLTEYS-SNKCSKPNVQKLKWMVSGRTARQLKHSYYEITHLPTI
          VECLQK.SK.NGRDL..W.EL.S.CL.E.S..NKCSKPNVQ.....VSG.T...LK.SY..ITHLPTI
Retrocopy VECLQKQSKTNGRDLNIW*ELISQCLNE*S<INKCSKPNVQRSR-IVSGSTTWKLKYSYHRITHLPTI

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
SRP012922_ascending_colon	0.00 RPM	27.61 RPM
SRP012922_cerebellum	0.00 RPM	16.91 RPM
SRP012922_heart	0.00 RPM	54.76 RPM
SRP012922_kidney	0.00 RPM	29.84 RPM
SRP012922_liver	0.00 RPM	18.58 RPM
SRP012922_lung	0.00 RPM	36.81 RPM
SRP012922_quadricep_muscle	0.00 RPM	641.28 RPM
SRP012922_spleen	0.00 RPM	44.30 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1275 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000001502	1 retrocopy	retro_dnov_2629,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275 ,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,