RetrogeneDB ID: retro_dnov_403

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4427:4247..5036(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSDNOG00000012883
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_dnov_403
AAACTACAGCCGGGTTCAGTGAAGGTCCGTGAGTCCTCATTACACCGGCCTCAGCTGGAGAACACTGGCAACTTTACTGA
AGCTCTTCAGGCTTATGGAACGAAGCCACGTGACATATTTGAAGCAAACGATCTTTTTGAGAATGGAAACATGACGCAGG
TTCAGGCGGCACTGGTGGCTCTTGCGGGTCTGGCTGAAACAGAAGGATTCCATACAACCATCAACATCGGCGTGAGGGAT
GCAGAAAAACAGGCAAGACGTTTTGATGAGGGAAAATTAAAAGCTGGTCAAAGTGTCATTGGCTTGCAGATGGGAACCAA
CAAGTGTGCCAGCCAAGCAGGTGTGACAGCCTATGGGCCAGGAGACATCTTTATGATCCCAAGACGCAAACTGACGAACC
TCGTGATCAGACCACAGTGAGCCTGCAGACGGGCACTAACCAAGGAGCAGCCAGGCAGGAAAGTTAGCCCAGGTACCAGG
AGGGACGGCTACGATCAGAAGCTGACACCACAGCCAGTGGACGACGCGGCGATTTCTCTGCAGATGGGGACCAACAAAGT
TGCTTCCCAGAAAGGAATGAGTGCGTACGGGCTTGGGCGGCAAGTATACGATCCCAAACACCGTGCTGCTCCGACAGAAC
CCGTCATTCCCAGCGGAAGCCAAGGAACAGGAGCAAATGGGTCAGAAATCAGTGACAGCGACGATCAGGCAGGACACCCC
GACGCCTCTCACGGCGAGGACCAAGAGGACTACCCCGGAAAGCGCCAGTACGGGGACCAAGGCTCTGAT

Alignment

ORF - retro_dnov_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.63 %
• Parental protein coverage: 65.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLQPGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKG
          KLQPGSVK.V.ESSL..PQLEN.GNF..A.QAYG.KP.DIFEANDLFENGNMTQVQ..LVALAGLA.T.G
Retrocopy KLQPGSVK-VRESSLHRPQLENTGNFTEALQAYGTKPRDIFEANDLFENGNMTQVQAALVALAGLAETEG

Parental  FHT-IDIG-EYAEKQ-RRFDXXXXXXXXXXXXXXMGTNKCASQAGMTAYG-TRRHLYDPKMQTDKPFDQT
          FHT.I.IG...AEKQ.RRFD..............MGTNKCASQAG.TAYG..RRHLYDPK.QTD.P.DQT
Retrocopy FHTTINIGVRDAEKQARRFDEGKLKAGQSVIGLQMGTNKCASQAGVTAYG<ARRHLYDPKTQTDEPRDQT

Parental  TISLQMGTNKGA-SQAGMLA-PGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDP
          T.SLQ.GTN.GA.SQAG.LA.PGTRRD.YDQKLT.QPVD...ISLQMGTNKVASQKGMS.YGLGRQVYDP
Retrocopy TVSLQTGTNQGA<SQAGKLA<PGTRRDGYDQKLTPQPVDDAAISLQMGTNKVASQKGMSAYGLGRQVYDP

Parental  KYCAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYQDDYPRDYQYGDQGID
          K..AAPTEPVI..GSQGTG.NGSEISDSD.QA..PD..HGE.Q.DYP...QYGDQG.D
Retrocopy KHRAAPTEPVIPSGSQGTGANGSEISDSDDQAGHPDASHGEDQEDYPGKRQYGDQGSD

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	0.19 RPM	140.99 RPM
SRP012922_cerebellum	0.14 RPM	78.22 RPM
SRP012922_heart	0.00 RPM	30.16 RPM
SRP012922_kidney	0.27 RPM	133.06 RPM
SRP012922_liver	0.00 RPM	72.45 RPM
SRP012922_lung	0.92 RPM	197.47 RPM
SRP012922_quadricep_muscle	0.17 RPM	22.67 RPM
SRP012922_spleen	0.23 RPM	171.23 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_403 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus	ENSDNOG00000012883	3 retrocopies	retro_dnov_223, retro_dnov_403 , retro_dnov_815,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mustela putorius furo	ENSMPUG00000003332	1 retrocopy	retro_mputfur_896,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,