RetrogeneDB ID: retro_dnov_986

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_13017:25836..26575(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSDNOG00000014778
• Aliases: None
• Description: NECAP endocytosis associated 1 [Source:HGNC Symbol;Acc:24539]

Sequence

>retro_dnov_986
TCCAACCATGGCTACAGGGCATCTGACTGGAAATTAGACCATCATGATTGGACTGGTTGCCTCTGAATGACTTCAAAAGG
GAAGATTGCCTATATCACTTGAGGATAAAGTTTCAGGGGAGTTCTGTGCTCCAGGACCAGTAGAACACTATCCCGGCATT
GCTGTGGAGATTGTTACAGATTCCAGCCACTGCTTTGCGATTTAGCTCCAGGATGGCACTGGGCACAGTGCTTTCATTGG
CATTGGCCTCACAGATTGGGGTGATGCTTTCAACTCTAACGTCTCCTTGCAAGGTCATTCCAAGTCAGTAAGTGGGAATC
TGATATTTCCAAACAATCTTGGGAAATGGACACACACCCCAAGTTAGATCTGAGCTTGAAGGAAGGACAGACCATCAGGT
TGAGTACAGGAAACATTACACAAAGGAAGGAGGTGCTTCTAAGCCCAAGATCTCAGGAGCTGGGGGGCCTAAACTTACTC
TCACCCCCACCTGCAGGCAAAGTCCCTATTCCTCCACCATCCTCCTCAGTTGCCATCAGTATTCATGTCACCCTACCCCA
TTCGAAAATCTAACCATGGAGGCAATGATGCAGGTATTCTTTTAGATATGGATTCTTCTGCTGCTGTCACACCAGCACCA
GAGCCAGTTTATGCAGGCAACGACTTGTGGGAAGATTTTAGCACTGCATCCAGCTCTGTTTCAAACCAGGCACCACAGCC
ATCCAACTGGGTCCAGTTC

Alignment

ORF - retro_dnov_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 90.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SNRGYRASDWKLDQPDWTGRLRITSK-GKIAYIKLEDKVSGELFAQAPVEQYPGIAVETVTDSSRYFVIR
          SN.GYRASDWKLD..DWTG.L..TSK.G....I.LEDKVSGE..A..PVE.YPGIAVE.VTDSS..F.I.
Retrocopy SNHGYRASDWKLDHHDWTGCL*MTSK>GRLP-ISLEDKVSGEFCAPGPVEHYPGIAVEIVTDSSHCFAI*

Parental  IQDGTGRSAFIGIGFTDRGDAFDFNVSLQDHFKWV-KQESEISKESQEMDTRPKLDLGFKEGQTIKLSIG
          .QDGTG.SAFIGIG.TD.GDAF..NVSLQ.H.K.V.K.ES.ISK.S.EMDT.PKLDL..KEGQTI.LS.G
Retrocopy LQDGTGHSAFIGIGLTDWGDAFNSNVSLQGHSKSV<KWESDISKQSWEMDTHPKLDLSLKEGQTIRLSTG

Parental  SIT-TKKGGTSKPKTSGTGG-LSLLPPPPGGKVTIPPLSSSVAI-SNHVTPPPIPKSNHGGSDADILLDL
          .IT.TK.GG.SKPK.SG.GG.L.LL.PPP.GKV.I.P..SS....S....P.PI.KSNHGG.DA.ILLD.
Retrocopy NIT<TKEGGASKPKISGAGG>LNLLSPPPAGKVPI-PPPSSSVA>SVFMSPYPIRKSNHGGNDAGILLDM

Parental  DSPAPVTTPAPAPVSAGNDLWGDFSTASSSVSNQAPQPSNWVQF
          DS.A.VT.PAP.PV.AGNDLW.DFSTASSSVSNQAPQPSNWVQF
Retrocopy DSSAAVT-PAPEPVYAGNDLWEDFSTASSSVSNQAPQPSNWVQF

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	24.89 RPM
SRP012922_cerebellum	0.00 RPM	106.81 RPM
SRP012922_heart	0.00 RPM	7.19 RPM
SRP012922_kidney	0.00 RPM	10.68 RPM
SRP012922_liver	0.00 RPM	14.71 RPM
SRP012922_lung	0.00 RPM	12.07 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.44 RPM
SRP012922_spleen	0.11 RPM	21.06 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_986 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986 ,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Oryctolagus cuniculus	ENSOCUG00000004309	1 retrocopy	retro_ocun_606,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,