RetrogeneDB ID: retro_dnov_2250

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_58417:1070..1622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: M6PR
• Ensembl ID: ENSDNOG00000003538
• Aliases: None
• Description: mannose-6-phosphate receptor (cation dependent) [Source:HGNC Symbol;Acc:6752]

Sequence

>retro_dnov_2250
ATGCAGATCAGCGAAGCTAATGGGAAGCAGATGTGGTGGGAAGACTCACCAGACTCATTTTCAATGGAAGTAATTGGGTC
CTGCTGATCTCTAAAGCGGGTGATGAATATGACAGTCAGTGTGGCAAGGAGCAGTGCCGTGCAGTGGTGATGATCTCCTG
CAATCGATATACCCTGGCGGACAATTTTAACCCTGTACTGAGGAATGAGGAAAAGTCCAAGATTGTTTCTACCTCTGCAA
GATGGTTGGTGGCCTGGCTTGTTCCCCAGCGGTCTCTCACCTCGGTGTGGGCTCTGTGTTACTTACCACATTGGCACCAC
TGGTCACTGTCTATATTACTGGGGGGTCCGGTCCCAGCGACTGGTGGTGAGAGCCAAGGGAATGGAGCAGTTTTCCCACT
TAGCCTTCTGGGAGGATCTTGGCAACCTGGTAGCAGATGGTTGTGACTTTGTTTGCCACTCTAAACCTCGAAATATGCCT
GCTGCTTATCGTGGTGTGGGGGATGACCTGCTGGGGGAGGATTCAGAAGAAAGGGATGACCATTTATTACCA

Alignment

ORF - retro_dnov_2250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.54 %
• Parental protein coverage: 66.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQINKSNGKET-VVGRLNETHIFNGSNWIMLIYKGGDEYDNHCGKEQRRAVVMISCNRHTLADNFNPV-S
          .QI...NGK...VVGRL....IFNGSNW..LI.K.GDEYD..CGKEQ.RAVVMISCNR.TLADNFNPV..
Retrocopy MQISEANGKQM<VVGRLTRL-IFNGSNWVLLISKAGDEYDSQCGKEQCRAVVMISCNRYTLADNFNPV<T

Parental  EERGKVQDCFYLFEMDSSLACSPEISHLSVGSVLLITFASLVAVYIIG-GFLYQRLVVGAKGMEQFPHLA
          EE.GKVQDCFYL..M...LACSP..SHL.VGSVLL.T.A.LV.VYI.G.G...QRLVV.AKGMEQF.HLA
Retrocopy EE*GKVQDCFYLCKMVGGLACSPAVSHLGVGSVLLTTLAPLVTVYITG<GVRSQRLVVRAKGMEQFSHLA

Parental  FWQDLGNLVA--CDFVCHSKP-NVPAAYHGVGDDQLREESEERDDHLLP
          FW.DLGNLVA..CDFVCHSKP.N.PAAY.GVGDD.L.E.SEERDDHLLP
Retrocopy FWEDLGNLVADGCDFVCHSKPRNMPAAYRGVGDDLLGEDSEERDDHLLP

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	0.78 RPM	75.45 RPM
SRP012922_cerebellum	0.27 RPM	32.03 RPM
SRP012922_heart	0.23 RPM	12.07 RPM
SRP012922_kidney	0.27 RPM	23.00 RPM
SRP012922_liver	0.93 RPM	37.00 RPM
SRP012922_lung	1.68 RPM	66.28 RPM
SRP012922_quadricep_muscle	0.35 RPM	10.21 RPM
SRP012922_spleen	1.95 RPM	94.20 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_2250 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003538	1 retrocopy	retro_dnov_2250 ,
Mus musculus	ENSMUSG00000007458	1 retrocopy	retro_mmus_2192,
Oryctolagus cuniculus	ENSOCUG00000017823	1 retrocopy	retro_ocun_1931,
Otolemur garnettii	ENSOGAG00000005610	1 retrocopy	retro_ogar_629,
Tarsius syrichta	ENSTSYG00000005689	2 retrocopies	retro_tsyr_1665, retro_tsyr_882,