RetrogeneDB ID: retro_dnov_2016

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_42416:11977..13358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018474
• Aliases: None
• Description: None

Sequence

>retro_dnov_2016
ATGAACAACTTCAGTAATGAGGAGTTTGACTGCCATTTCCTTGATGAAGGTTTTACTGCCAAGGACATTCTGGACCAAAA
AATTAATGAAGTTTCTTCTGATGATGATAAAGATGCCTTCTATGTTGCGGACCTTGGAGACATTCTAAAGAAACATCTGA
GATGGTTAAAAGTTCTTCCTCGTGTCACCCCCTTCTTTGCAGTCAAATGTAATGACAGTAAAGCCATAGTGAAGACCCTG
GCTTCCATAGGGACAGGATTTGATTGAGCTAGCAAGACTGAAATCCAGTTGGTGCAGAGTCTCGGGGTGCCACCAGAGAG
GATAATCTATGCAAACCCTTGTAAACAAGTGTCTCAAATTAAGTATGCCGCCAATAATGGTGTTGAGATGATGACTTTTG
ACAGCGAGGTTGAGTTGATGAAAGTGGCCAGGGCACATCCAAAGGCAAAAGTTGGTTTTGTGGATTGCCACCGATGACTC
CAAAGCAGTCTGCCACTCAGTGTTAAATTTGGAGCCACACACAAAACCAGCAGGCTTCTTTTGGAATGGGCTAAAAAGCT
CGATATTGATGTCATTGATGTCAGCTTCCATGTGGGAAGTGGCTATACTGATCCTGAAACTTTTGTGCAGGCCATCTCTG
ATGCCCACTGTGTCTTTGACATGGGAGCTGAGGTTGGTTTCAGCATGTATCTGCTTGATATTGATGATGGCTTTCCCAGA
ACTGATGATGTGATGCTTAAATTTGGAGAGATAACCAGTGTCATTAATCCAGCATTAGGCAAGTATTTCCCATTAGATTC
TGGAGTGAGAATCATAGCTGAACCAGGCCGATATTATGTTGCTTCAGCTTTCACACTTGCAGTGAATATCATTGCCAAAA
AAATTGTATTTAAGGAACACAGGCTCTGGTGATGAAGATGAATCGAGTGAACAAACCTTTATGTATTATGTGAATGATGG
AGTATATGGATCATTTAATTGTATCCTTTATGGTCATGAGCATGTAAAGCCTCTTCTGCAGAAGAGATGCAAACCAGATG
AGAAGTATTACTCATCTAGCATATGGGGACCCACGTGTGATGGCCTCGATCGGATCGTTGAGTGCTGTGGCCTGCCGGAA
ATGCACGTGGGCGACTGGATGCTGTTTGAGAACATGGGGGCTTACACTGTAGCTACTGCTTCCACTTTCAATGGGTTCCA
GAGGCCAACCATCTACTACGTGATGTCAGGGCCTGCATGGCAAGTCATGCAACAAATCGAGATCGGGGGGTTTCCACCCA
AAGTAGAGGAGCAAGATGCCAGTGCTCTGTCTTTTTCCTGTGCTTGGGAAAGTGGGATGAAGCACCACCTGGCCACTTGT
GCTCCAGCTAGTATTAATGTG

Alignment

ORF - retro_dnov_2016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNNFSNEEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKVLPRVTPFYAVKC
          MNNFSNEEFDCHFLDEGFTAKDILDQKINEVSS.DDKDAFYVADLGDILKKHLRWLKVLPRVTPF.AVKC
Retrocopy MNNFSNEEFDCHFLDEGFTAKDILDQKINEVSSDDDKDAFYVADLGDILKKHLRWLKVLPRVTPFFAVKC

Parental  NDSKAIVKTLASIGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVEMMTFDSEVELM
          NDSKAIVKTLASIGTGFD.ASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVEMMTFDSEVELM
Retrocopy NDSKAIVKTLASIGTGFD*ASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVEMMTFDSEVELM

Parental  KVARAHPKAK-LVLRIATDDSKAVCR-LSVKFGATLKTSRLLLERAKELDIDVIGVSFHVGSGCTDPETF
          KVARAHPKAK.LVL.IATDDSKAVC..LSVKFGAT.KTSRLLLE.AK.LDIDVI.VSFHVGSG.TDPETF
Retrocopy KVARAHPKAK>LVLWIATDDSKAVCH<LSVKFGATHKTSRLLLEWAKKLDIDVIDVSFHVGSGYTDPETF

Parental  VQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSDDVKLKFEEITSVINPALDKYFPSDSAVRIIAEPGRY
          VQAISDA.CVFDMGAEVGFSMYLLDI..GFP..DDV.LKF.EITSVINPAL.KYFP.DS.VRIIAEPGRY
Retrocopy VQAISDAHCVFDMGAEVGFSMYLLDIDDGFPRTDDVMLKFGEITSVINPALGKYFPLDSGVRIIAEPGRY

Parental  YVASAFTLAVNIIA-KKIVFKQQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKXXXPD
          YVASAFTLAVNIIA.KK......TGS.DEDESSEQTFMYYVNDGVYGSFNCILY.H.HVKPLLQK...PD
Retrocopy YVASAFTLAVNIIA>KKL-YLRNTGSGDEDESSEQTFMYYVNDGVYGSFNCILYGHEHVKPLLQKRCKPD

Parental  EKYYSSSIWGPTCDGLDRIVERCGLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQVM
          EKYYSSSIWGPTCDGLDRIVE.CGLPEMHVGDWMLFENMGAYTVA.ASTFNGFQRPTIYYVMSGPAWQVM
Retrocopy EKYYSSSIWGPTCDGLDRIVECCGLPEMHVGDWMLFENMGAYTVATASTFNGFQRPTIYYVMSGPAWQVM

Parental  QQIKSRGFPPEVEEQDASALPFSCAWESGMKRHPATCAPASINV
          QQI...GFPP.VEEQDASAL.FSCAWESGMK.H.ATCAPASINV
Retrocopy QQIEIGGFPPKVEEQDASALSFSCAWESGMKHHLATCAPASINV

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	0.78 RPM	36.95 RPM
SRP012922_cerebellum	0.41 RPM	12.10 RPM
SRP012922_heart	0.00 RPM	6.26 RPM
SRP012922_kidney	0.27 RPM	22.45 RPM
SRP012922_liver	0.00 RPM	6.97 RPM
SRP012922_lung	0.92 RPM	19.40 RPM
SRP012922_quadricep_muscle	0.17 RPM	3.12 RPM
SRP012922_spleen	1.26 RPM	57.69 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_2016 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 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016 , retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,