RetrogeneDB ID: retro_dnov_1520

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_225134:358..1122(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000017317
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_dnov_1520
ATGGGCCAGTGCAGCATCACCTCCTCCTCTGAAACTGTGCTCGTCTTTCTCAACCTCAACTTCTGGAGGGCAGCTGGTAT
TTTATGCTATGTAGGAGCCTACGTGTTCATCACTTATGACGACTGTGACCACTCTTTTGAAGATGTGTACACTCTCATCC
CTGCTGTAGTGATCATAGCTGTAGGAGACCTGCTTTCCATTATTGGGCTAGTTGGCTGCTGCGCCACAATCCGGGAAAGC
CACTGTGGACTTGCCACGGTTACCATCCTCCTCCTCTTGATTTTTGTTACGGAAGTTGTTGTTGTTGTGGTTTTGGGATA
TGTTTGCAGACCAAAGGTGGAAAATGAGGTGGATTGCAGCATTTCAGAAATTATATAAGACCTACAAGGGAACCAACTCT
GATGCTGCTAGTCGGGCTATTGATTATGTGCAGAAACAGCTGCACGTTGTGGAATTCACAACTACTCAGACTGGGAAAAT
ACAGACTGTTTTAAAGAAACCAAAAACCAGAGTGTCCCTCTTAGCTGTTGTAGAGACACTGCCATCAGCTGTAATGGCAG
TCTGGCCCACCCTTCTGACGTCTATGCTGAGGGTGTGAGGCTCTGGTTTTGAAGAAGCTACAGGAAATTATGATGCATGT
TATCTGGGCAGCACTAGCATTTGCAGCTATTCAGCTGCTGGGCATGCTGTGTGCGTGCATTGTGTTGTGCAGAAGGAGAA
GAAATCCTGCTTATGAGCTCCTCATCATTGGCAGAACCTATGCG

Alignment

ORF - retro_dnov_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGQCGITSS-KTVLVFLNLIFWGAAGILCYVGAYVFITYDDYDHFFEDVYTLIPAVVIIAVGALLFIIGL
          MGQC.ITSS..TVLVFLNL.FW.AAGILCYVGAYVFITYDD.DH.FEDVYTLIPAVVIIAVG.LL.IIGL
Retrocopy MGQCSITSSSETVLVFLNLNFWRAAGILCYVGAYVFITYDDCDHSFEDVYTLIPAVVIIAVGDLLSIIGL

Parental  IGCCATIRESHCGLATFVIILLLVFVTE-VVVVVLGYVYRAKXXXXXXXXI-QKVYKTYNGTSPDAASRA
          .GCCATIRESHCGLAT..I.LLL.FVTE.VVVVVLGYV.R.K........I.QK.YKTY.GT..DAASRA
Retrocopy VGCCATIRESHCGLATVTILLLLIFVTEVVVVVVLGYVCRPKVENEVDCSI>QKLYKTYKGTNSDAASRA

Parental  IDYVQRQLHC-CGIHNYSDWENTDWFKETKNQSVPLSCCRDTAISCNGSLAHPSDLYAE-GCEALVVKKL
          IDYVQ.QLH..CGIHNYSDWENTD.FKETKNQSVPLSCCRDTAISCNGSLAHPSD.YAE.GCEALV.KKL
Retrocopy IDYVQKQLHV<CGIHNYSDWENTDCFKETKNQSVPLSCCRDTAISCNGSLAHPSDVYAE<GCEALVLKKL

Parental  QEIMMHVIWAALAFAAIQLLGMLCACIVLCRRSRDPAYELLITGGTYA
          QEIMMHVIWAALAFAAIQLLGMLCACIVLCRR.R.PAYELLI.G.TYA
Retrocopy QEIMMHVIWAALAFAAIQLLGMLCACIVLCRRRRNPAYELLIIGRTYA

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	0.19 RPM	127.77 RPM
SRP012922_cerebellum	0.00 RPM	143.93 RPM
SRP012922_heart	0.00 RPM	39.21 RPM
SRP012922_kidney	0.27 RPM	192.75 RPM
SRP012922_liver	0.00 RPM	71.83 RPM
SRP012922_lung	0.00 RPM	132.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	105.75 RPM
SRP012922_spleen	0.23 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_1520 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,