RetrogeneDB ID: retro_dnov_1482

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_21426:13602..14178(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCCPDH
• Ensembl ID: ENSDNOG00000016354
• Aliases: None
• Description: saccharopine dehydrogenase (putative) [Source:HGNC Symbol;Acc:24275]

Sequence

>retro_dnov_1482
CTGACCACTAGGGAGAGTTTCCTGACTGCACACTCAGAACCTGGGGGAATGTGCAGTCATGATGTACCTGGAAGTCAGCA
ACTGATGGTTCTGGAGATCAGAGTAATATGGAAAAACTATGAAATGAGTCAAACCGGAAACCTGTTTCATTCGTTGGTCC
AAAATTGGAAAGCAGGTGGCCAACTTCTCACTGTAGAGAACTCAACACATACACATTCCTTTCTTGGGAGCTGACACATT
TGTTGTGAAACGGACTCAGCGTCACTTGCATGAAAATCTAGAGGAATCACCAGTTCAATATGGTGCTTATGTGACTGTGG
AGGCATCACCTCTGCTATTAAGCTGATGTTGGCAGGAATTTTCTTTTTGTTCTTTGTTGAGGTTTACCATTGGAAGGCAA
CTTCTCATAAAATTCCTGTGACTCTTCTCCTTTGGTTATGTTTCAAGACAAGGCCCAACCCAAAAACAGATTGATGCCTC
ATCATTCACAATGACGTTCTTTGGTCAAGGATATAGCCAAAGCCTTTGTACTGATAAGAGAAACCCAATATCAGAATTCG
TTCTCGGGTGAAAGGA

Alignment

ORF - retro_dnov_1482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.21 %
• Parental protein coverage: 52.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LTAVESFLTLHVGPEGMCIHDG-TWKSAVNGFGDRSNLKILRNESNLKPVPFVGPKLKRR-PISYCRELS
          LT..ESFLT.H..P.GMC.HD..TWKSA..G.GD.SN...L.NESN.KPV.FVGPKL..R.P.S.CREL.
Retrocopy LTTRESFLTAHSEPGGMCSHDV<TWKSATDGSGDQSNMEKL*NESNRKPVSFVGPKLESRWPTSHCRELN

Parental  TYT-IPFLRSDVSVVKRTQRYLHENLEETPVQYAAYVTMER-ITSVIKLMFAGFLFSFFV-KFSIGRQLL
          TYT.IPFL..D..VVKRTQR.LHENLEE.PVQY.AYVT.E..ITS.IKLM.AG..F.FFV..F.IGRQLL
Retrocopy TYT<IPFLGADTFVVKRTQRHLHENLEESPVQYGAYVTVEA<ITSAIKLMLAGIFFLFFV>RFTIGRQLL

Parental  IKFPWLFSFGYFSKQGPTQKQIDSASFTMTFFGQGYSQGLPTDK-SKPNIRICTQVKG
          IKF..LFSFGY.S.QGPTQKQID..SFTMTFFGQGYSQ.L.TDK..KPNIRI...VKG
Retrocopy IKFL*LFSFGYVSRQGPTQKQIDASSFTMTFFGQGYSQSLCTDK<EKPNIRIRSRVKG

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	92.37 RPM
SRP012922_cerebellum	0.00 RPM	70.38 RPM
SRP012922_heart	0.00 RPM	57.08 RPM
SRP012922_kidney	0.00 RPM	285.02 RPM
SRP012922_liver	0.00 RPM	1488.47 RPM
SRP012922_lung	0.00 RPM	49.02 RPM
SRP012922_quadricep_muscle	0.00 RPM	246.13 RPM
SRP012922_spleen	0.00 RPM	85.16 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_1482 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015884	1 retrocopy	retro_cfam_842,
Dasypus novemcinctus	ENSDNOG00000016354	1 retrocopy	retro_dnov_1482 ,
Monodelphis domestica	ENSMODG00000006356	1 retrocopy	retro_mdom_553,