RetrogeneDB ID: retro_dnov_1511

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_22090:41181..42027(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSDNOG00000013620
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_dnov_1511
CTGGCAGATGAACTGGTTCTTGTGGATGTCATAGAAGACAAATTGAAGGGAGAGATGATGATCTCCAACCTGGCACCCTT
TTCCTTAGAACACCAACCATTGTCTCTGGCAAAGACTATAGTGTGACTGCAAACTTCAAGTTGGTTATTATCACAGCTGG
GGCACATCAGCAAGAGGGAGAAAGCCATTTTAATTTGGTCCAGCATAACGTAAACATCTTTAAACTCATCATTGCTAATA
TTGTAAAATACAGCCCGAACTGCAAGTTGCTTGTTGTTTCCAATCCAGTGGATATCTTGACCTTTGTGGCTTGGAAACAA
GTGGCTTTCCCAAAAACCATGTTATTGGAAGTGATTGCAATCTGGATTCAGCCTGGTTCCCTTACCTAATGGAGGAGAGG
CTGGAGGTTCACCCATTAAGCTGTCATGGATGGGTCCTTGGGGAACATTGAGACTCTGGTGTGCCTGTGTGGAGTGGCGT
GAATGGTGCTGGTGTTTCCTTGAAAAAGCTGCAGCCTGATTGAGACACTGAAGCAGATAAGTAACAGTGGAAAGAGGTTC
ACAAACAGGTGGTTGACAGTGCTTATGAGGTGCTCAAACTGAAAGGCTATACTTCATGGGTCATTGGACTGTCTGTGGCA
GATTTGACAGAAACTCTAATCAAGAATCTTAGATGTGTACATCCAATTTCTACCATGATTAAGGAAGTCTATGGAATAAA
AGGTGATGTCTTTCTTAGAGTTCCTTGCATCTTGGACAGAATGGAATCTTAGATGTTGCCAAGGTGTTACTGCCTGCTGA
AGAAGAGACCCATTTGAAGAAGAGTGCAGATACACTTTGGGGGATC

Alignment

ORF - retro_dnov_1511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.43 %
• Parental protein coverage: 97.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTDELALVDVLEDKLKGEMM-DLQHGSLFLQTPKIVADKDYSVTANSKVVVVTAGVRQQEGESRLNLVQR
          L.DEL.LVDV.EDKLKGEMM.DLQ.G.LFL.TP.IV..KDYSVTAN.K.V..TAG..QQEGES..NLVQ.
Retrocopy LADELVLVDVIEDKLKGEMM<DLQPGTLFLRTPTIVSGKDYSVTANFKLVIITAGAHQQEGESHFNLVQH

Parental  NVNVFKFIIPQIIKYSPDCIIIVVSNPVDILTYVTWK-LSGLPKHRVFGSGCNLDSARFRYLMAEKLGVH
          NVN.FK.II..I.KYSP.C...VVSNPVDILT.V.WK..SG.PK..V.GS.CNLDSA.F.YLM.E.L.VH
Retrocopy NVNIFKLIIANIVKYSPNCKLLVVSNPVDILTFVAWK<TSGFPKNHVIGSDCNLDSAWFPYLMEERLEVH

Parental  PTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPDMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWA
          P.SCHGW.LGEH.DS.V.VWSGVN.AGVSL..L.PD..T..D...WKEVHK.VV.SAYEV.KLKGYT.W.
Retrocopy PLSCHGWVLGEH*DSGVPVWSGVNGAGVSLKKLQPD*DTEADK*QWKEVHKQVVDSAYEVLKLKGYTSWV

Parental  IGLSVADLIESLFKNLSRIHPVSTMVKGMYGIENEVFLSLPCILN-ARGLTSVINQKLKDDEVAQLKKSA
          IGLSVADL.E.L.KNL...HP.STM.K..YGI...VFL..PCIL....G...V....L...E...LKKSA
Retrocopy IGLSVADLTETLIKNLRCVHPISTMIKEVYGIKGDVFLRVPCILD<QNGILDVAKVLLPAEEETHLKKSA

Parental  DTLWDI
          DTLW.I
Retrocopy DTLWGI

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	299.29 RPM
SRP012922_cerebellum	0.00 RPM	408.56 RPM
SRP012922_heart	0.00 RPM	1695.69 RPM
SRP012922_kidney	0.00 RPM	900.24 RPM
SRP012922_liver	0.00 RPM	13.47 RPM
SRP012922_lung	0.00 RPM	184.19 RPM
SRP012922_quadricep_muscle	0.00 RPM	987.97 RPM
SRP012922_spleen	0.00 RPM	156.93 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_1511 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 19 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511 , retro_dnov_1570, retro_dnov_529,
Dasypus novemcinctus	ENSDNOG00000018915	11 retrocopies	retro_dnov_1063, retro_dnov_1366, retro_dnov_1429, retro_dnov_1707, retro_dnov_1848, retro_dnov_2417, retro_dnov_362, retro_dnov_669, retro_dnov_797, retro_dnov_821, retro_dnov_887,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Microcebus murinus	ENSMICG00000017183	2 retrocopies	retro_mmur_275, retro_mmur_300,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pteropus vampyrus	ENSPVAG00000002462	3 retrocopies	retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus	ENSRNOG00000013000	3 retrocopies	retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,