RetrogeneDB ID: retro_dnov_265

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3134:67070..67522(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK1
• Ensembl ID: ENSDNOG00000018590
• Aliases: None
• Description: cyclin-dependent kinase 1 [Source:HGNC Symbol;Acc:1722]

Sequence

>retro_dnov_265
TTGTATAAGGGGAAACACAAGACTACAGGTCAAGTGGTAGCCATGAGGAAAATCAGACTAGAAAGTGAAGAGGAAGGGGT
TCCTTGTACTGCAATTTGGGAAATTTCCCTATAAAAGAACTTCGTCCTTCAAATATAGTCAGTCTTCAAGATGTGCTTAT
GCAGGATTCCAGGTTATATCTCATCTTTGAATTTCTTTCCACTGAGCTCCAGAAATACTTGGATTCTGTCCCACCTAGTC
AGTTCATGGATTTCTCACTTGTTAAGAATTATTTATACCTAATCCTACAAGGGATTGTGTTTTGTCACTCTAGAACAGTT
CTTCACAGAGACTTAAAACCTCAACATCTATTGATTGATGACAAAGGAACAATTAAATTAGCTGATTTTGGGTTTGCCAG
AACTTTCGGAATACCTATCAGAGTATATACACATAAAGTGGTAATGCTCTGG

Alignment

ORF - retro_dnov_265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 53.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISL-LKELRHPNIVSLQDVLMQDSRLYLIFEFLSMD
          .YKG.HKTTGQVVAM.KIRLESEEEGVP.TAI.EISL..KELR..NIVSLQDVLMQDSRLYLIFEFLS..
Retrocopy LYKGKHKTTGQVVAMRKIRLESEEEGVPCTAIWEISL<IKELRPSNIVSLQDVLMQDSRLYLIFEFLSTE

Parental  LKKYLDSIPPGQFMDSSLVKVKAQSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARA
          L.KYLDS.PP.QFMD.SLVK.....YLY.ILQGIVFCHSR.VLHRDLKPQ.LLIDDKGTIKLADFG.AR.
Retrocopy LQKYLDSVPPSQFMDFSLVK----NYLYLILQGIVFCHSRTVLHRDLKPQHLLIDDKGTIKLADFGFART

Parental  FGIPIRVYTHEVVTLW
          FGIPIRVYTH.VV.LW
Retrocopy FGIPIRVYTHKVVMLW

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	12.83 RPM
SRP012922_cerebellum	0.00 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.15 RPM
SRP012922_lung	0.00 RPM	1.22 RPM
SRP012922_quadricep_muscle	0.17 RPM	0.52 RPM
SRP012922_spleen	0.34 RPM	28.27 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_265 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000014245	1 retrocopy	retro_dnov_145,
Dasypus novemcinctus	ENSDNOG00000018590	1 retrocopy	retro_dnov_265 ,
Equus caballus	ENSECAG00000009716	1 retrocopy	retro_ecab_637,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702,
Rattus norvegicus	ENSRNOG00000000632	1 retrocopy	retro_rnor_1638,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309, retro_tbel_807, retro_tbel_812,
Tursiops truncatus	ENSTTRG00000001085	2 retrocopies	retro_ttru_1619, retro_ttru_1634,