RetrogeneDB ID: retro_dnov_1616

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24758:83100..83503(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSDNOG00000005619
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_dnov_1616
TTAATGAAATTATATAAGACCTACAAGGGAACCAACCCCGATGCTGCTAGTCGGGCTATTGATTATGTGCAGAAACAGCT
GCACGTTGTGGAATTCACAACTACTCAGACTGGGAAAATACAGACTGATTTAAAGAAACCAAAATCCAGAGTGTCCCTCT
TAGCTGTTGTAGAGACACTGCCATCAGCTGTAATGGCAGTCTGGCCCACCCTTCTGACGTCTATGCTGAGGGTGTGAGGC
TCTGGTTTTGAAGAAGCTACAGGAAATTATGATGCATGTTATCTGGGCAGCACTAGCATTTGCAGCTATTCAGCTGCTGG
GCATGCTGTGTGCGTGCATTGTGTTGTGCAGAAGGAGAAGAAATCCTGCTTATGAGCTCCTCATCATTGGCAGAACCTAT
GCG

Alignment

ORF - retro_dnov_1616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.59 %
• Parental protein coverage: 53.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IQKVYKTYNGTSPDAASRAIDYVQRQLHC-CGIHNYSDWENTDWFKETKNQSVPLSCCRDTAISCNGSLA
          ..K.YKTY.GT.PDAASRAIDYVQ.QLH..CGIHNYSDWENTD.FKETK.QSVPLSCCRDTAISCNGSLA
Retrocopy LMKLYKTYKGTNPDAASRAIDYVQKQLHV<CGIHNYSDWENTD*FKETKIQSVPLSCCRDTAISCNGSLA

Parental  HPSDLYAEG-CEALVVKKLQEIMMHVIWAALAFAAIQLLGMLCACIVLCRRSRDPAYELLITGGTYA
          HPSD.YAEG.CEALV.KKLQEIMMHVIWAALAFAAIQLLGMLCACIVLCRR.R.PAYELLI.G.TYA
Retrocopy HPSDVYAEG<CEALVLKKLQEIMMHVIWAALAFAAIQLLGMLCACIVLCRRRRNPAYELLIIGRTYA

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	127.77 RPM
SRP012922_cerebellum	0.14 RPM	143.93 RPM
SRP012922_heart	0.00 RPM	39.21 RPM
SRP012922_kidney	0.00 RPM	192.75 RPM
SRP012922_liver	0.15 RPM	71.83 RPM
SRP012922_lung	0.00 RPM	132.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	105.75 RPM
SRP012922_spleen	0.00 RPM	91.23 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_1616 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616 ,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,