RetrogeneDB ID: retro_dnov_568

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6272:71948..72432(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC2
• Ensembl ID: ENSDNOG00000013708
• Aliases: None
• Description: ER membrane protein complex subunit 2 [Source:HGNC Symbol;Acc:28963]

Sequence

>retro_dnov_568
TGGCTCCTATAAGAACAAGTGGTGAATCCTGCCTTAGACTATGGTTGGGGTGACGTGGCATTGTTTGTCTGCAGGAATTG
AAAAGGCAGTTCCCTGGCAGTCACAGAGTCAAGCAACTAACTGGAATGCGATTAGAACCCATGGAAAGATATGATAATGC
CTAACAGCTTTATGACAGAATTTTACAAGAAGATCCAATTAATACTGTGGCAAGAGAGCTAAGAGCGCCATTTGAAAAAG
TCCAGGGGAAAAATGTGGAGACCATTCGGGAGCTGAACGAGTATCTGGAATAATTGTTGGAGACCAATAAGCCTGGCATG
AACTTGTAGAACTTTATATCAAGGAACATGACTATGCAAAGCAGCCTTTTGTCTAGAGGAGCTTATGGCCACTAATCCAC
ACAATCACGTATACTGCCAGCAGTATGCTGAAGTTAAATTTACCCAGGCGTGGACTTGAAAACCTTGAACTTTCAAGAAA
GTAT

Alignment

ORF - retro_dnov_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 57.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WIIYEQVMIAALDCGRDDLALF-CLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNT
          W...EQV...ALD.G..D.ALF.CLQEL.RQFPGSHRVK.LTGMR.E.MERYD.A.QLYDRILQEDP.NT
Retrocopy WLL*EQVVNPALDYGWGDVALF<CLQELKRQFPGSHRVKQLTGMRLEPMERYDNA*QLYDRILQEDPINT

Parental  AARKRKIAIRKAQGKNVEAIRELNEYLE-QFVGDQEAWHELAELYINEHDYA-KAAFCLEELMMTNPHNH
          .AR.......K.QGKNVE.IRELNEYLE...VGDQ.AWHEL.ELYI.EHDYA.KAAFCLEELM.TNPHNH
Retrocopy VARELRAPFEKVQGKNVETIRELNEYLE<IIVGDQ*AWHELVELYIKEHDYA<KAAFCLEELMATNPHNH

Parental  LYCQQYAEVKYTQG-GLENLELSRKY
          .YCQQYAEVK.TQ..GLENLELSRKY
Retrocopy VYCQQYAEVKFTQA>GLENLELSRKY

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	32.87 RPM
SRP012922_cerebellum	0.00 RPM	26.67 RPM
SRP012922_heart	0.00 RPM	50.58 RPM
SRP012922_kidney	0.00 RPM	45.18 RPM
SRP012922_liver	0.00 RPM	18.11 RPM
SRP012922_lung	0.00 RPM	40.17 RPM
SRP012922_quadricep_muscle	0.00 RPM	42.75 RPM
SRP012922_spleen	0.00 RPM	43.72 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_568 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726,
Dasypus novemcinctus	ENSDNOG00000013708	1 retrocopy	retro_dnov_568 ,