RetrogeneDB ID: retro_dnov_1915

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_36438:2766..3595(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GORASP2
• Ensembl ID: ENSDNOG00000007263
• Aliases: None
• Description: golgi reassembly stacking protein 2, 55kDa [Source:HGNC Symbol;Acc:17500]

Sequence

>retro_dnov_1915
TCTGAAGATCTGTTCAGCCTTATTGAAACACATGAAGCAAAACCGTTGAAACTTTATGTGTACAACACAGATACCGATAA
CTGTCGAGAAGTGATTATTACACCAAATTCTGCATGGGGTGGAGAAGGAAGCTAGGATGTGGCATTGGATATGGCTATTT
GCATCGAATACCTACATGCCCGTTTGAAGAAGGAAAGAAAATTTCTCTTCTAGGACAAATGACTGGTACACCTATTACTC
CTCTTAAAGATGGGTTTACAGAGGTCCAGCTGTCCTCAGTTAATCCTCCATCTCTGTCAGCTCCAGGAACTACGAGAATT
GAACAAAGTCTGTCTGGACTTTCTATTAGCTCAACTTCACTAGTCAGTAATGTTCTAAGTACAGGTGTACCAACAGTACC
ATTATTGTCACCACAAGTAAACCAATCCCTCACGTCTGTGCCACCAATGAACCCAACTAGTACATTACCAGGTCTGATGC
CTTTACCAGCGGGACTCCCTGACCTCCCCACCCTCCCCAATCTCAACCTCCCCACACACACATCATGCCAGGTGTGGGCT
TAGCGGAAATCGTGAACCCGGGTTTGCCACCTCTTCCTTCCTTGCCTCCCCAAGACTTACCTGGCATTGCACCTCTCCCT
ATGCCATCCAAGTTCCTTCCGCCATTCCCTTTGGTTCCAGAAGTTTCTTCTGCAGCAAGCTCTGGGGAGCTGCTGTCTTC
CCTTCCACCCACCGGCAACCCACCCTCTGACCCTGTCATGACTACTGCCACGGCAGACGCTGTCTCCTCACTCACAGTGG
ATGTGATGTCCCCTCCTGCAAATGCCCCC

Alignment

ORF - retro_dnov_1915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.21 %
• Parental protein coverage: 61.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEDLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGS-LGCGIGYGYLHRIPTRPFEEGKKIS
          SEDLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGS.LGCGIGYGYLHRIPT.PFEEGKKIS
Retrocopy SEDLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGS<LGCGIGYGYLHRIPTCPFEEGKKIS

Parental  LPGQMTGTPITPLKDGFTEVQLSSVNPPSLSPPGTTGIEQSLSGLSISSTSPVVSNVLSTXVPTVPLLSP
          L.GQMTGTPITPLKDGFTEVQLSSVNPPSLS.PGTT.IEQSLSGLSISSTS..VSNVLST.VPTVPLLSP
Retrocopy LLGQMTGTPITPLKDGFTEVQLSSVNPPSLSAPGTTRIEQSLSGLSISSTS-LVSNVLSTGVPTVPLLSP

Parental  QVNQSLTSVPPMNPTSTLPGLMPLPAGLPDLPTLPNLNIPT-PHIMPGVGLAEIVNPGLPPLPSLPSRDL
          QVNQSLTSVPPMNPTSTLPGLMPLPAGLPDLPTLPNLN.PT..HIMPGVGLAEIVNPGLPPLPSLP..DL
Retrocopy QVNQSLTSVPPMNPTSTLPGLMPLPAGLPDLPTLPNLNLPT<THIMPGVGLAEIVNPGLPPLPSLPPQDL

Parental  PGIAPLPMPSNFLPPFPLVPEVSSAARSGELLSSLPPTGNPPSDPVMTSATLDAVSSLTLDVMSPLANAP
          PGIAPLPMPS.FLPPFPLVPEVSSAA.SGELLSSLPPTGNPPSDPVMT.AT.DAVSSLT.DVMSP.ANAP
Retrocopy PGIAPLPMPSKFLPPFPLVPEVSSAASSGELLSSLPPTGNPPSDPVMTTATADAVSSLTVDVMSPPANAP

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	17.70 RPM	36.56 RPM
SRP012922_cerebellum	11.96 RPM	21.58 RPM
SRP012922_heart	6.03 RPM	10.67 RPM
SRP012922_kidney	9.04 RPM	13.69 RPM
SRP012922_liver	13.93 RPM	37.15 RPM
SRP012922_lung	10.54 RPM	23.37 RPM
SRP012922_quadricep_muscle	14.02 RPM	24.58 RPM
SRP012922_spleen	10.42 RPM	22.89 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_1915 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	ENSDNOG00000007263	1 retrocopy	retro_dnov_1915 ,
Mustela putorius furo	ENSMPUG00000000812	1 retrocopy	retro_mputfur_676,
Sorex araneus	ENSSARG00000007686	1 retrocopy	retro_sara_305,
Tarsius syrichta	ENSTSYG00000014516	1 retrocopy	retro_tsyr_1657,