RetrogeneDB ID: retro_dnov_1479

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_21329:80229..81515(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000010938
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000002180
• Aliases: None
• Description: None

Sequence

>retro_dnov_1479
TATGACAAAGTTCTGAAGAAAGGAAAGACCAAGAAAGCTCTAAAAGATTTTGAGAAATTATGGGTGATCCTACTGCAGCA
TTAGAAAAATTGAAGAAAATCTGAAAGGCCAGAATAATGGAGCAAATGAGGCTTAAGCACCAGAAGAGTGAGAAATGGGC
CAACCCAAGGGTAATTATGACCAGATATGACCTGGAGGTTCACCAAGCTAAGCAGGAACAACTGGCCAAGAACAAAGAAC
TGACACAGGAACTCCAGGCAGCATCTGAGAATGAGGAAGAGGAGGGAGTTGAAGAAGAAGATGGATTCCTGGTCCCTGAT
GTAGTAAATGAAGTACAAATGAATACAGATGGACTGAATCCCTGGATGCTCAGAAGTTGGACCAGTGATACAGAAGAGGC
CAAGTCCAGAAGTACCCTGAACAGCTGCCAGAGCCATTGGCCCATGAAGATTCTGAAAATGAGGGAGAGGGAAAGACCAG
CGGAAACCAAAGAAGAGATTTTGTTGAAAGAATTTGCAGAAAGGTGAGTCTTTAGAAAAAGGTCTGAGCTTAACCAGGAT
TCTGAGTTGCTGGGTAGTCAAGAAACAAAAGATCCTAGCACCCAGGAGGTGCTGTTTGAATTGAGGGCACTGTCCTGGAA
TCTCAACAAGGAAAATCACTAGTTGAGGGAGTCAAAGTGAACTCAGTGGGGACTATTCATCTAGTTCAGAGAGAGAAACC
TGTCCAGGAAGAGTCCGAGGAGCCCCTGTTGCTACAGAGGCTGGAGAGAGTACAAATTCTGGAAGAGCTAGAAAAACTGG
GCAAAGAAAGGTGATTTCAAAATAAGGAGTTCCCCACACCTGTGTTAGAAGGGCAACCATAAGAAAGGATCTCAAATGAT
CAACCAGGTGCCCCTAAGGAGAAGAAAAAGGAGCAAATGATTGATCTAAGGAGCCTCCTAATCACAAAGTCTCCTTCTGT
TAAGTTTTTGGCAGTTCCCACATGACAGAGGAGTTGGAAGATAAAGGCGAGGCAGAGCAAAAGCAAATGATAAAGGAAGC
TTTTGCTGGGGATGGTGTCATTAGAGACTTGAAAGAAAAAAGGGAAGCTGTGGAAGCAAGCAAGCCCAGGGATGTGGACC
TGACATTGCCTGGCTGGGTCAAGTGCGGTGGCACAGGCCTAAAACCCAGTGCCAAGAAAAGATGCCATTTTCTCATGAAA
ACCCCTGGGGGTTCTACAAGAAAAGACAAGAATTTGCCAAATTGATTATCAATGAAAAGTGCAACATCCATGCAGCAGCT
CTTCAG

Alignment

ORF - retro_dnov_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.12 %
• Parental protein coverage: 56.02 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  YHKVLKKG-KAKKALKDFENLRKVDPSAALEELEKIEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEAR
          Y.KVLKKG.K.....K.F......DP.AALE.L.KI.KAR.ME.M.LKHQ.S.KWA....IM..YDLE..
Retrocopy YDKVLKKG<KDQESSKRF*EIMG-DPTAALEKLKKI*KARIMEQMRLKHQKSEKWANPRVIMTRYDLEVH

Parental  QAMQEQLAKNKELTQKLQVASESEEEEGGGEEHGLLVPDAVNEVQMNTDGPNPWMHRSWTSDAKEA-EVQ
          QA.QEQLAKNKELTQ.LQ.ASE.EEEEG..EE.G.LVPD.VNEVQMNTDG.NPWM.RSWTSD..EA..VQ
Retrocopy QAKQEQLAKNKELTQELQAASENEEEEGVEEEDGFLVPDVVNEVQMNTDGLNPWMLRSWTSDTEEA<QVQ

Parental  KNPEQLSEPVANKDSESEGE-ERPAVAEEEILLKEFAERRAFRKRSELNQDPEPLGSQETKDSSSQEVLS
          K.PEQL.EP.A..DSE.EGE.ERPA...EEILLKEFAER..FRKRSELNQD.E.LGSQETKD.S.QEVL.
Retrocopy KYPEQLPEPLAHEDSENEGE>ERPAETKEEILLKEFAER*VFRKRSELNQDSELLGSQETKDPSTQEVLF

Parental  ELRALSQKLNKENHQSRKP-KGSSAGTVRLVQREEPVQEESEEPLLLQRPERVHTQEELEELDKEGCFQS
          ELRALS..LNKENH..R...K..S.GT..LVQRE.PVQEESEEPLLLQR.ERV...EELE.L.KE..FQ.
Retrocopy ELRALSWNLNKENH*LRES<KVNSVGTIHLVQREKPVQEESEEPLLLQRLERVQILEELEKLGKER*FQN

Parental  KELPRPVLEGQPLERITNYQPGAPKEKKKKEQMIDLKNLLTTKSPSVKSLAVPT-TIEEMEDKEEAEQKQ
          KE.P.PVLEGQP.ERI.N.QPGAPKE.KKKEQMIDL..LL.TKSPSVK.LAVPT...EE.EDK.EAEQKQ
Retrocopy KEFPTPVLEGQP*ERISNDQPGAPKE-KKKEQMIDLRSLLITKSPSVKFLAVPT<MTEELEDKGEAEQKQ

Parental  MIKEAFAGDDVIRDFLKEKREAVEASKPKDMDLTLPGWGEWGGAGLKPSAKKRRRFLFKTPEGPPRKDKN
          MIKEAFAGD.VIRD.LKEKREAVEASKP.D.DLTLPGW...GG.GLKPSAKKR..FL.KTP.G..RKDKN
Retrocopy MIKEAFAGDGVIRD-LKEKREAVEASKPRDVDLTLPGWVKCGGTGLKPSAKKRCHFLMKTPGGSTRKDKN

Parental  LPN-VIINEKRNIHAAAHQ
          LPN..IINEK.NIHAAA.Q
Retrocopy LPN<LIINEKCNIHAAALQ

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	26.64 RPM
SRP012922_cerebellum	0.00 RPM	22.27 RPM
SRP012922_heart	0.46 RPM	11.83 RPM
SRP012922_kidney	0.00 RPM	14.51 RPM
SRP012922_liver	0.31 RPM	7.74 RPM
SRP012922_lung	0.15 RPM	41.08 RPM
SRP012922_quadricep_muscle	0.00 RPM	27.00 RPM
SRP012922_spleen	0.11 RPM	40.86 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_1479 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479 ,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,