RetrogeneDB ID: retro_dnov_223

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2727:6614..7566(-)
• 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_223
GTCTCAGCTGATATCAAGAACAGGATTGCATCCAAGTAGGATCATTTGGCAGAAGATCTTCACAGCTGGATAGAAGAGGT
GACTGGCATGAGCATTGGCACCAACTTTCAATTGGGCCTGAAAAATGGCATAATCCTCTGCGAACTCATAAACTACAGCC
CAGCCAGGTGCACTGAAGAAGGTCAATGAGCCCTCATTAAAGTGGCCTCAGGTGGAGAATATTGGCAACTTTATTCAAGG
TATTCAGGCTAAGGTATGATGCCATGTGACATATTTGAAGCAAATGATCTTTTTTCAGAATGGAAATATGACCCAGGTTC
ATACTACGCTGGTGGCTCTTGCAGGTCTGGCTAAGAGAAAAGGATTCCATACAACCACTGACATGGGAGTTAAGTATGCA
GAAAAACAAACAAGACATTTTGACGAAGGAAAATTAAAAGTTGCCCAGAGTGCAACTGGCTTGCAGTTGGGAACCAACAT
ATGTGCCAGCCAGGCAAGTATGACAGCCTATGGGACCAGGAGGCATCTTTATGACCCCAAGATGCAAATTGACAAACCTT
TTGACCAGATCATGATTAATCTGCAGATGGGCACTAACGAAGGAGCCAGCCAGGCAGGGATGTTAGCATCATGTACCAGA
AGAGATGTCTATGATCAGAGGCTAACCTTACAACCAGTGGACAACAAGACGATTTCTCTACAGACTGGGACCAACAGAGT
TACTTCCCAGAAAGGAATGAGTATATATGGGCTTGGGCAGCAAGGATATGATCCTGAGTACTGTGCTGTTCCAGCAGAAC
CTGTCGTTCTCAATGGAAGCCAAGGAACAGGAACAAATGGGTCAGAAGTCAGTGATAGCGATTATCAGGCAGAATATCCC
AATGAATATCATGGCAAATACTAAGATGACTACCCCAGAGATTGCCAATATGGGGACCAAGGTATTGATTAT

Alignment

ORF - retro_dnov_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.01 %
• Parental protein coverage: 79.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSAEVKNKIASKYDHQAEEDLRSWIEEVTGMSIGTNFQLGLKDGIILCELIN-KLQPGSVKKVNESSLNW
          .SA..KN.IASK.DH.AE.DL.SWIEEVTGMSIGTNFQLGLK.GIILCELIN...QPG..KKVNE.SL.W
Retrocopy VSADIKNRIASK*DHLAE-DLHSWIEEVTGMSIGTNFQLGLKNGIILCELIN>TAQPGALKKVNEPSLKW

Parental  PQLENIGNFIKAIQAY-GMKPHDIFEANDLF-ENGNMTQVQTTLVALAGLAKTKGFHTI-DIG-EYAEKQ
          PQ.ENIGNFI..IQA..GM.P.DIFEANDLF..NGNMTQV.TTLVALAGLAK.KGFHT..D.G..YAEKQ
Retrocopy PQVENIGNFIQGIQAK<GMMPCDIFEANDLF>QNGNMTQVHTTLVALAGLAKRKGFHTTTDMGVKYAEKQ

Parental  -RRFDXXXXXXXXXXXXXXMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAG
          .R.FD...............GTN.CASQA.MTAYGTRRHLYDPKMQ.DKPFDQ..I.LQMGTN.GASQAG
Retrocopy TRHFDEGKLKVAQSATGLQLGTNICASQASMTAYGTRRHLYDPKMQIDKPFDQIMINLQMGTNEGASQAG

Parental  MLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPVIHNGSQGT
          MLA..TRRD.YDQ.LTLQPVDN.TISLQ.GTN.V.SQKGMS.YGLG.Q.YDP.YCA.P.EPV..NGSQGT
Retrocopy MLASCTRRDVYDQRLTLQPVDNKTISLQTGTNRVTSQKGMSIYGLGQQGYDPEYCAVPAEPVVLNGSQGT

Parental  GTNGSEISDSDYQAEYPDEYHGEYQDDYPRDYQYGDQGIDY
          GTNGSE.SDSDYQAEYP.EYHG.Y.DDYPRD.QYGDQGIDY
Retrocopy GTNGSEVSDSDYQAEYPNEYHGKY*DDYPRDCQYGDQGIDY

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	140.99 RPM
SRP012922_cerebellum	0.14 RPM	78.22 RPM
SRP012922_heart	0.00 RPM	30.16 RPM
SRP012922_kidney	0.00 RPM	133.06 RPM
SRP012922_liver	0.00 RPM	72.45 RPM
SRP012922_lung	0.00 RPM	197.47 RPM
SRP012922_quadricep_muscle	0.00 RPM	22.67 RPM
SRP012922_spleen	0.11 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_223 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,