RetrogeneDB ID: retro_dnov_2600

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8935:83903..84340(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN7L3
• Ensembl ID: ENSDNOG00000003379
• Aliases: None
• Description: ataxin 7-like 3 [Source:HGNC Symbol;Acc:25416]

Sequence

>retro_dnov_2600
GAGGAATTTGAGATTATGGAACAGACAGGGATATTCATCTTTGAAAAGGTTCTCAACCAATGCAAGTGAAAGTAGTGTGT
TTACCCAATTGCAGCCACAGCATTGCTGCCTCCTGCTCTGCTCCCCATCTGGAGAAGTGCCTGGAAATGTGTGGAACAGC
AGCCGCAGCCTCCAGGTTGCCAAAAGCAACAGTATGAACAAGTCTGAAAGTGACCAAGTGGACGATGATGACATCAATGA
CAACGACTGCTCCTGTAGATCGAGAAGAAATCCAAGAAGAGAAACTTGTTACAAATGGCAATTCCACTTGAAGATCCAAG
TCTTAAAAACACAAAAACTGGGAGTTTAGCAATTCAGATCCTTTTAAGCATAACAACTCCACTGGAATGAGCTATGGGAC
CCTGGAGCCAGAGCAGCTGTGTAGCCTGCTCACCACG

Alignment

ORF - retro_dnov_2600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.36 %
• Parental protein coverage: 81.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDFEIVDQPGLDIFGQVFNQWKSKECV-CPNCSRSIAASRFAPHLEKCLGMGR-NSSRIANRRIANSNNM
          ..FEI..Q.G..IF..V.NQ.K.K.CV..PNCS.SIAAS..APHLEKCL.M...NSSR......A.SN.M
Retrocopy EEFEIMEQTGIFIFEKVLNQCK*K*CV<LPNCSHSIAASCSAPHLEKCLEMCG<NSSR--SLQVAKSNSM

Parental  NKSESDQEDNDDINDNDWSYGS-EKKAKKR-KSDKNPNSPRRSKSLKHKNGELSNSDPFKYNNSTGISYE
          NKSESDQ.D.DDINDND.S..S.EKK.KKR.K...N.NS..RSKS.KHKN.E.SNSDPFK.NNSTG.SY.
Retrocopy NKSESDQVDDDDINDNDCSCRS<EKKSKKR<KLVTNGNST*RSKS*KHKNWEFSNSDPFKHNNSTGMSYG

Parental  TLGPEELRSLLTT
          TL.PE.L.SLLTT
Retrocopy TLEPEQLCSLLTT

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	6.22 RPM
SRP012922_cerebellum	0.00 RPM	10.59 RPM
SRP012922_heart	0.00 RPM	2.32 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	3.41 RPM
SRP012922_lung	0.00 RPM	5.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	4.92 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_2600 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 5 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003379	13 retrocopies	retro_dnov_1026, retro_dnov_1144, retro_dnov_1211, retro_dnov_1590, retro_dnov_1902, retro_dnov_2325, retro_dnov_2448, retro_dnov_2497, retro_dnov_2600 , retro_dnov_516, retro_dnov_86, retro_dnov_867, retro_dnov_961,
Homo sapiens	ENSG00000087152	1 retrocopy	retro_hsap_4847,
Gorilla gorilla	ENSGGOG00000010959	1 retrocopy	retro_ggor_3023,
Myotis lucifugus	ENSMLUG00000006416	1 retrocopy	retro_mluc_41,
Macaca mulatta	ENSMMUG00000029935	1 retrocopy	retro_mmul_820,