RetrogeneDB ID: retro_dnov_107

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1620:155928..156578(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHA3
• Ensembl ID: ENSDNOG00000002717
• Aliases: None
• Description: pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3 [Source:HGNC Symbol;Acc:14338]

Sequence

>retro_dnov_107
GAGGCGGCTCTGTACAAGTGGACCAACTAGCTCACAGGTTGGCAGCCTCGTTGCTTTGTTTTAGATAATGGAATCCTATC
CTACTATGAGTCACAGGATGTTTGTAAAGGAAGCAAAGGAAGTATAAAGATGGCAGTTTGTGAAATTAAAGTCCATTCAG
CAGACAACACAAGATGGAATTAATCATTCCGGGAGAGCAGCACTTCTACATGAAAGCGGTGACTGCGGCTGAAAGACAGA
GGTGGCTGGTTGCTCTGGGGAGCGCCAAAGCCTGTTTGACTGATACTAGGACTAAGAAAGAAAAAGAAATAAGTGAAACC
AGTGAATCTCTGAAAACCAAAGTGTCTGAACTCCGCCTCTACTGTGACCTCCTAATGCAGCAAGTTCATACAACCCAAGA
GCTTGTTCACCACGGTAAGAGTCATTCATCTTCCAGTGTGGAGAACACGAGTGAAGCCCCCTCTTTGCTTAGTGCCACCT
GTAATACCTTCATCACAACACTTGAGGACTGTGTGAAGATAGCAAATGCCAAGTTTAAACCCGAGATGTTTCAACTGCCC
CATCCGGATCCCTTAGTTTCTCCTGCATCACCTTCCCCTGTTCAAATGATGAAGCGTTCTGTCAGCCACCCTGGTTCTCG
CAACTCAGAG

Alignment

ORF - retro_dnov_107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.04 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGVLYKWTNYLTGWQPRWFVLDNGILSYYDSQDDVCKGSKGSIKMAVCEIKVHSADNTR-MELIIPGEQH
          E..LYKWTN.LTGWQPR.FVLDNGILSYY.SQD.VCKGSKGSIKMAVCEIKVHSADNTR.MELIIPGEQH
Retrocopy EAALYKWTN*LTGWQPRCFVLDNGILSYYESQD-VCKGSKGSIKMAVCEIKVHSADNTR<MELIIPGEQH

Parental  FYMKAVNAAERQRWLVALGSSKACLTDTRTKKEKEISETSESLKTKMSELRLYCDLLMQQVHTIQEFVHH
          FYMKAV.AAERQRWLVALGS.KACLTDTRTKKEKEISETSESLKTK.SELRLYCDLLMQQVHT.QE.VHH
Retrocopy FYMKAVTAAERQRWLVALGSAKACLTDTRTKKEKEISETSESLKTKVSELRLYCDLLMQQVHTTQELVHH

Parental  DENHSFSNKENMNEASSLLSATCNTFITTLEDCVKIANAKFKPEMFQLPHPDPLVSPVSPSPVQMMKRSV
          ...HS.S..EN..EA.SLLSATCNTFITTLEDCVKIANAKFKPEMFQLPHPDPLVSP.SPSPVQMMKRSV
Retrocopy GKSHSSSSVENTSEAPSLLSATCNTFITTLEDCVKIANAKFKPEMFQLPHPDPLVSPASPSPVQMMKRSV

Parental  SHPGSCSSE
          SHPGS..SE
Retrocopy SHPGSRNSE

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	0.97 RPM	4.86 RPM
SRP012922_cerebellum	3.71 RPM	9.21 RPM
SRP012922_heart	2.09 RPM	4.64 RPM
SRP012922_kidney	3.29 RPM	7.12 RPM
SRP012922_liver	1.24 RPM	4.95 RPM
SRP012922_lung	5.50 RPM	18.02 RPM
SRP012922_quadricep_muscle	0.35 RPM	1.56 RPM
SRP012922_spleen	5.72 RPM	19.23 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_107 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013997	5 retrocopies	retro_chof_1366, retro_chof_1559, retro_chof_300, retro_chof_736, retro_chof_985,
Cavia porcellus	ENSCPOG00000003906	1 retrocopy	retro_cpor_487,
Dasypus novemcinctus	ENSDNOG00000002717	1 retrocopy	retro_dnov_107 ,
Erinaceus europaeus	ENSEEUG00000004169	1 retrocopy	retro_eeur_416,
Homo sapiens	ENSG00000116095	1 retrocopy	retro_hsap_2060,
Macropus eugenii	ENSMEUG00000015317	2 retrocopies	retro_meug_1530, retro_meug_341,
Microcebus murinus	ENSMICG00000009898	1 retrocopy	retro_mmur_617,
Myotis lucifugus	ENSMLUG00000005823	2 retrocopies	retro_mluc_1031, retro_mluc_689,
Oryctolagus cuniculus	ENSOCUG00000005495	1 retrocopy	retro_ocun_1273,
Otolemur garnettii	ENSOGAG00000002724	1 retrocopy	retro_ogar_1845,
Tupaia belangeri	ENSTBEG00000007550	3 retrocopies	retro_tbel_4186, retro_tbel_4555, retro_tbel_4723,
Tarsius syrichta	ENSTSYG00000005341	1 retrocopy	retro_tsyr_869,
Tursiops truncatus	ENSTTRG00000009729	2 retrocopies	retro_ttru_1296, retro_ttru_1497,
Vicugna pacos	ENSVPAG00000003490	3 retrocopies	retro_vpac_487, retro_vpac_578, retro_vpac_619,