RetrogeneDB ID: retro_dnov_1210

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_163889:64..824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC7
• Ensembl ID: ENSDNOG00000012405
• Aliases: None
• Description: DEP domain containing 7 [Source:HGNC Symbol;Acc:29899]

Sequence

>retro_dnov_1210
AAGGCGGCGGCACTGAACTCGGCTCTCCAGAGCCCCGCGCAGAGGCCTCCAGGTTTCACTGTGGCCCAGAAGCTATTTGG
AGCCACATATATATGGAGCAGCATTATAAGCACCCTTCACGCACAGGTGGAAGTGAAGAGACGAAGACACCATTTAAAAT
GGCACAATGACTGCTTTGTTGGTTCAGAAGCTGTGGATGTCATTTTTTCTCACCTAATTCAGAATAAGTATTTTGGTGAT
GTAGATATTCCTCGGGCCAAAGTGGTGAAAGTGTGTCAAGCACTTACGGACTACAAAGTGTTTGAAGCAGTTCCAACCAA
AGTCTTTGGAAAAGACAAAAAACCTACATTTGAAGATAGTAGTTGCAGCCTTTATAGGTTTACCACAATACCTGACAAAA
GACAGTCAGTTAGGCAAAGAGAACAAACTATATTCACCTTCCAGGTATGCAGAAGCATTATTTAAGTCATCTGATTTGAA
ATCAGCAAGTTTAGAGGATCTGTGGAAAAATCTGAGTTTAAAGCCAGCTAACTTCCCTAATGTAAATAGCTCTACAACCC
TGTCTCCAGAAGTTATTAATGAAGTATGGCAAGAGGAAACAATTGGGCGCCTATTACAACTTGTAGACCTTCCACTTCTT
GAGTCCTTACTCAAACAGCAAGAGGTTGTACCTAAAGTTCCTCAACCCAAGAGGCATCCTGACTTGATCTACGATAGTAG
CTATCTGGATCGAGGGATTCTCAAGGCTTATAGCGACTCT

Alignment

ORF - retro_dnov_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.21 %
• Parental protein coverage: 50.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTAAPKADTPSPSALCPKPPXXXVAQKPFGATYIWSSIISTLHAQVEVKRRRHHLKRHNDCFVGSEAVDV
          K.AA......SP......PP...VAQK.FGATYIWSSIISTLHAQVEVKRRRHHLK.HNDCFVGSEAVDV
Retrocopy KAAALNSALQSPAQ---RPPGFTVAQKLFGATYIWSSIISTLHAQVEVKRRRHHLKWHNDCFVGSEAVDV

Parental  IFSHLIQNKYFGDVDIPRAKVVKVCQALMDYKVFEAVPTKVFGKDKKPTFEDSSCSLYRFTTIPD-QDSQ
          IFSHLIQNKYFGDVDIPRAKVVKVCQAL.DYKVFEAVPTKVFGKDKKPTFEDSSCSLYRFTTIPD..DSQ
Retrocopy IFSHLIQNKYFGDVDIPRAKVVKVCQALTDYKVFEAVPTKVFGKDKKPTFEDSSCSLYRFTTIPD>KDSQ

Parental  LGKENKLYSPSRYAEALFKSSDLKSASL-DLWKNLSLKPANFPXXXXXXXXXXXXIGEVWREETIGRLLQ
          LGKENKLYSPSRYAEALFKSSDLKSASL.DLWKNLSLKPANFP............I.EVW.EETIGRLLQ
Retrocopy LGKENKLYSPSRYAEALFKSSDLKSASLEDLWKNLSLKPANFPNVNSSTTLSPEVINEVWQEETIGRLLQ

Parental  LVDLPLLESLLRQQEVVPKVPQPKRPPDLIYDSSYLDRGILKAYSDS
          LVDLPLLESLL.QQEVVPKVPQPKR.PDLIYDSSYLDRGILKAYSDS
Retrocopy LVDLPLLESLLKQQEVVPKVPQPKRHPDLIYDSSYLDRGILKAYSDS

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	4.47 RPM	3.11 RPM
SRP012922_cerebellum	0.14 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.55 RPM	3.01 RPM
SRP012922_liver	10.53 RPM	8.98 RPM
SRP012922_lung	0.92 RPM	0.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.23 RPM	0.00 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_1210 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	ENSDNOG00000012405	1 retrocopy	retro_dnov_1210 ,
Echinops telfairi	ENSETEG00000017093	1 retrocopy	retro_etel_1447,
Loxodonta africana	ENSLAFG00000008704	1 retrocopy	retro_lafr_539,
Monodelphis domestica	ENSMODG00000009718	1 retrocopy	retro_mdom_1180,