RetrogeneDB ID: retro_dnov_1121

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_150304:3789..4522(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSDNOG00000005048
• Aliases: None
• Description: major facilitator superfamily domain containing 1 [Source:HGNC Symbol;Acc:25874]

Sequence

>retro_dnov_1121
ATTGGTGGGGAGTCCTTAGCAGTGGCCCAGAATACATATGCTGTGAGTTGGTTTAAAGGCAAAGAATTAAACCTGGTGTT
TGAACTGCAACTTACCATGGCTAGAATTGGAAGTACAGTAAACATGAACCTCATGGGATGGCAGTATTCTAAGATTGAAG
CTTCGCTGGGTTCTGCGGGTCATAACAACCCTTGGTGTCACACTTATGATCAGGGGTATAACATGTATTCTTTCACTAAT
CTCTGCCTTGGCCCTTGCTTACTTGGATCAGAGAGCAGAAAGAATTCTTCATAAAGAACAAGGAAAAACAGGTGAAGTTA
TTAAGCTGACTGATGTGAAGGACTTCTCCTTATCTCTGTGGCTCATATTTATCATCTGTGCCTGCTATTATGTAGTGGTG
TTCCCTTTTATTGGGCTGGGAAAAGTTTTCTTTACAGAGAAAGTTGGATTTTCCTCCCAGGCAGCAAGTGCGATTAACAG
TCTTGTATATGTCATATCAGCTCCCATGTCCCCAATATTTGGGATCCTGGTGGATAAAACAGGAAGAAACATCATTTGGG
TTCTGTGTGTGGTGGCAACCACTCTGGCTTCTCACATGATGTTGGCCTTTACTCTGTGGAACCCTTGGATTGCTATGTGC
CTCCTGGGACTCTCCTATTCATTGCTTGCCTGCGCACTGTGGCCAATGGTGGCCTTTGTGGTTCCTGAACATCAGCTGGG
AATTGCATATGGC

Alignment

ORF - retro_dnov_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.69 %
• Parental protein coverage: 52.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGGESLAVAQNTYAVSWFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKIEASLGSAGH-TTLGVTLM
          IGGESLAVAQNTYAVSWFKGKELNLVF.LQL.MARIGSTVNMNLMGW.YSKIEASLGSAGH.TTLGVTLM
Retrocopy IGGESLAVAQNTYAVSWFKGKELNLVFELQLTMARIGSTVNMNLMGWQYSKIEASLGSAGH>TTLGVTLM

Parental  IGGITCILSLISALALAYLDQRAERILHKEQGKTGEVIKLTDVKDFSLSLWLIFIICVCYYVVVFPFIGL
          I.GITCILSLISALALAYLDQRAERILHKEQGKTGEVIKLTDVKDFSLSLWLIFIIC.CYYVVVFPFIGL
Retrocopy IRGITCILSLISALALAYLDQRAERILHKEQGKTGEVIKLTDVKDFSLSLWLIFIICACYYVVVFPFIGL

Parental  GKVFFTEKFGFSSQAASAINSVVYVISAPMSPIFGILVDKTGRNIIWVLCAVATTLASHMMLAFTLWNPW
          GKVFFTEK.GFSSQAASAINS.VYVISAPMSPIFGILVDKTGRNIIWVLC.VATTLASHMMLAFTLWNPW
Retrocopy GKVFFTEKVGFSSQAASAINSLVYVISAPMSPIFGILVDKTGRNIIWVLCVVATTLASHMMLAFTLWNPW

Parental  IAMCLLRLSYSLLACALWPMMAFVVPEHQLRTAYG
          IAMCLL.LSYSLLACALWPM.AFVVPEHQL..AYG
Retrocopy IAMCLLGLSYSLLACALWPMVAFVVPEHQLGIAYG

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	12.83 RPM	19.45 RPM
SRP012922_cerebellum	5.64 RPM	10.04 RPM
SRP012922_heart	6.96 RPM	11.60 RPM
SRP012922_kidney	17.52 RPM	28.47 RPM
SRP012922_liver	8.98 RPM	11.15 RPM
SRP012922_lung	19.70 RPM	20.92 RPM
SRP012922_quadricep_muscle	8.65 RPM	7.27 RPM
SRP012922_spleen	18.20 RPM	30.45 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_1121 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121 ,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,