RetrogeneDB ID: retro_dnov_1964

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_39246:5105..6296(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC39A10
• Ensembl ID: ENSDNOG00000013599
• Aliases: None
• Description: solute carrier family 39 (zinc transporter), member 10 [Source:HGNC Symbol;Acc:20861]

Sequence

>retro_dnov_1964
TATATTGAGAAACTTTTTTATCTTTATGGTGAAAGCAGAAGACTGTTCTTTTTTGATCTGGAGAAACTTTTAACTAACTT
GGGCCTTAGAGAGATAAAAGTAATCAAGATTAATCATCAGGATCTTGGCCACGATCATGTTTCTCACTTAGATATTTTGG
CAGTTCTGGAGGGAAAGCATTTTCACTTGCATCACTACCAGCATTCCCATAATCATTTAAATTCAGAAAATCAGACTGTG
ACCAGTTTATCAACAAAAGGAAACCATAAATGTGATCCAGAGAAAGAACTAATTGAAATATCTATAAAATTTGCTGATAA
ACATATGCACAACCATAATCCTCACTTACATAATCGTCATTTGCATTATCACCTTGATCATAATGCTACTTACCATTTTC
ATAATGATTCTATTACTCAGAGTAATCACGGTGAACATAGCTATTAACCATCAATAAAGACCAATACAACACAGGAACAA
ACTGAAATTAACTGACTGCAACAAAAGAAGAAAAGAAAAGGGAAGAAAAGCAATGTGAATTTTGAGGTTATTATACCAGG
TTTCCCCTGTTAACCATGTTTAGGGTAAACATATTCAGGTCCACAAGCTTGATCATGTACATAATCCAGGTCATTCTCAT
GTACATGTTCCAGAACATAATGGTCATGAACCTGGTCATGGACACCAAGATCTCGAATCTGTTGAGGGTGAACTTCAACA
TATTAGAAAACGAGGAGCACCATATGTTTTAAAAAGTGCAATTTATCCAGCTGTTAGTCACAGATATCATCATGAAGATG
ACCATCAGCATGACGAGTGTTTAAACATCACTCAGTTAAGATACTATTGTCATCATGCCAACTCTCCGATCTCATCTGAT
CTATTTACGTAACTTCGCCTGCATTGTTATATCAAATTGACAGCCGACTCTGTATTGAGAATTTTGACAAACTTTTGGTT
GAAGATTTAAACAAAGGTAAAAATCTGGTTCCTGAAGATAAGGCACGTGTAGGTGCATCAGCTTGGATTTGTGGTATCAT
TTTTAATACTGTCATTAGTCTGCTTTCCTTGCTAGGCATGATCTTGGTTCCCACTATTAACCAAGGATGCTTCAAATTCC
TTCTCGCACTCCTTGTTGCACTAACTGTAGGAACAATGAGTGGAGATGCCCATCTTCATCTACTGCTCCAT

Alignment

ORF - retro_dnov_1964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 51.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YIEKLFDRYGENGRLSFFGLEKLLTNLGLGEIKIVEINHEDLGHDHVSHLDILAVLEGRHFHSHHHQHSH
          YIEKLF..YGE..RL.FF.LEKLLTNLGL.EIK...INH.DLGHDHVSHLDILAVLEG.HFH.HH.QHSH
Retrocopy YIEKLFYLYGESRRLFFFDLEKLLTNLGLREIKVIKINHQDLGHDHVSHLDILAVLEGKHFHLHHYQHSH

Parental  NHLNSENQTVTSLSTKRNHKCDPEKEIIEISVKSGDKHMHDHNHRLHNRHLHYHLDHNATHHFHNDSITQ
          NHLNSENQTVTSLSTK.NHKCDPEKE.IEIS.K..DKHMH.HN..LHNRHLHYHLDHNAT.HFHNDSITQ
Retrocopy NHLNSENQTVTSLSTKGNHKCDPEKELIEISIKFADKHMHNHNPHLHNRHLHYHLDHNATYHFHNDSITQ

Parental  SDHGEPSHEPSTKTNTTQEQTEIKPTKQKKKRKGKKSNVNFEVITPGF-PPNHVQGEHNRVHKLDHVHNP
          S.HGE.S..PS.KTNTTQEQTEI..............NVNFEVI.PGF.P.NHV.G.H..VHKLDHVHNP
Retrocopy SNHGEHSY*PSIKTNTTQEQTEIN*LQXXXXXXXXXXNVNFEVIIPGF>PVNHV*GKHIQVHKLDHVHNP

Parental  GHSHVHVPEHNGHEPGHGHQDLESDNEGELRHVKKREAPHVKKSAIYSAASHKDSNEDDRQHDECLNVTQ
          GHSHVHVPEHNGHEPGHGHQDLES..EGEL.H..KR.AP.V.KSAIY.A.SH....EDD.QHDECLN.TQ
Retrocopy GHSHVHVPEHNGHEPGHGHQDLES-VEGELQHIRKRGAPYVLKSAIYPAVSHRYHHEDDHQHDECLNITQ

Parental  LLRYYGHGANSPISPDLFTYL-CPALLYQIDSRLCIEHFDKLLVEDLNKDKNLVPED-AHIGASAWICGI
          .LRYY.H.ANSPIS.DLFT.L..PALLYQIDSRLCIE.FDKLLVEDLNK.KNLVPED.A..GASAWICGI
Retrocopy -LRYYCHHANSPISSDLFT*L<SPALLYQIDSRLCIENFDKLLVEDLNKGKNLVPEDKARVGASAWICGI

Parental  ISITVISLLFLLGVILVPIINQGCFKFLLTFLVALAVGTMSGDAFLHLLSH
          I..TVISLL.LLG.ILVP.INQGCFKFLL..LVAL.VGTMSGDA.LHLL.H
Retrocopy IFNTVISLLSLLGMILVPTINQGCFKFLLALLVALTVGTMSGDAHLHLLLH

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	14.00 RPM
SRP012922_cerebellum	0.14 RPM	45.50 RPM
SRP012922_heart	0.00 RPM	2.09 RPM
SRP012922_kidney	0.00 RPM	3.83 RPM
SRP012922_liver	0.00 RPM	0.77 RPM
SRP012922_lung	0.00 RPM	9.32 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.08 RPM
SRP012922_spleen	0.11 RPM	16.25 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_1964 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013599	1 retrocopy	retro_dnov_1964 ,
Dasypus novemcinctus	ENSDNOG00000018834	1 retrocopy	retro_dnov_1567,