RetrogeneDB ID: retro_dnov_2521

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_82296:923..1598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTSZ
• Ensembl ID: ENSDNOG00000012612
• Aliases: None
• Description: cathepsin Z [Source:HGNC Symbol;Acc:2547]

Sequence

>retro_dnov_2521
CGTGGGAGCCAGCTCTTGGGGCGCAGAACCTATTCCCGACTTCATGAGTACCTGTCTTCGAAGGAGCTGCTGGAGATCTG
GGACAGAAGCAACGTGATGAGCGTCAACTTCACCAGCATCCCCAGGAACCAGCACCTCCCCATTTCTGCGGCTCCTGCTG
GGCCCCGGCAGCACCAGCGCCTTGGAGGATGCATCACAGCAAGAGGAAGGGAGCGTGGCCCTCCACCCTGGTGTCCCTGC
AGAACCTCAGCTGAGAGGAGGCCTGCGCCTGCGAGGTGCGCACTGATCTGCTGCTGTGGGAGTACGTCCACAACCACGGC
ATCCGCGGTGAGACCTGCAGCAACTACCACACCAAGGACCAAGAGTGTAACAAGTTCAACTGGTGTGGGACTTGCACAGA
ATTCAGAGTGTGCCATGTCATCCAGAACTACTCCCGCTGGAGAGTGAGTGACTATGGCTCCCTCTGAACGAGACCAGATG
AGAGCAGAAATCTACAAAATGGCCCCATCAGCTGTGGAATAATAGCAGGAAAAGGGATGGATGAATACACTGGCTGGCAT
CTATACTAAATATAATTAGATACCCTTTATAAACTATATCATTTCTGTGAAAGGGTGGGATGTCAGCAAGGGGACCCAGT
ATTGGATTGTCAGGAATTCATGCTGTGAACCATGC

Alignment

ORF - retro_dnov_2521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 88.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGDQLLGRRTYPRPHEYLSPAELPQRWDWRNVNGVNYASVTRNQHI-PQYCGSCWA-HGSTSAMADR-IN
          RG.QLLGRRTY.R.HEYLS..EL...WD..NV..VN..S..RNQH..P..CGSCWA..GSTSA..D..I.
Retrocopy RGSQLLGRRTYSRLHEYLSSKELLEIWDRSNVMSVNFTSIPRNQHL<PHFCGSCWA<PGSTSALEDA<IT

Parental  IKRKGAWPP-TLLSVQNVIDCGQAGSCEGGTDLLVWAYAHSHGIPDETCNNYQAKDQECNKFNQCGTCTE
          .......PP.TL.S.QN......A..CE..TDLL.W.Y.H.HGI..ETC.NY..KDQECNKFN.CGTCTE
Retrocopy ARGRERGPP<TLVSLQN-LS*EEACACEVRTDLLLWEYVHNHGIRGETCSNYHTKDQECNKFNWCGTCTE

Parental  FKVCHVIQNYTLWRVGDYGSLSGREKMMAEIYANGPIRCGIMVNKGMDQ-TG-GLYTEYQ-APFINHVIS
          F.VCHVIQNY..WRV.DYGSL..R.........NGPI.CGI...KGMD..TG.G.YT.Y...PFIN..IS
Retrocopy FRVCHVIQNYSRWRVSDYGSL*TRPDESRNL-QNGPISCGIIAGKGMDEYTG>GIYTKYN*IPFINYIIS

Parental  VAGWGVSNGTEYWIVRNSWRDSC
          V.GW.VS.GT.YWIVRNS....C
Retrocopy VKGWDVSKGTQYWIVRNSCCEPC

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	109.10 RPM
SRP012922_cerebellum	0.14 RPM	1.92 RPM
SRP012922_heart	0.00 RPM	10.21 RPM
SRP012922_kidney	0.00 RPM	13.69 RPM
SRP012922_liver	0.00 RPM	64.55 RPM
SRP012922_lung	0.00 RPM	18.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.54 RPM
SRP012922_spleen	0.23 RPM	60.44 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_2521 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Dasypus novemcinctus	ENSDNOG00000012612	1 retrocopy	retro_dnov_2521 ,
Felis catus	ENSFCAG00000000845	1 retrocopy	retro_fcat_383,
Monodelphis domestica	ENSMODG00000016601	1 retrocopy	retro_mdom_1021,