RetrogeneDB ID: retro_dnov_227

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2757:42998..43311(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36AL
• Ensembl ID: ENSDNOG00000015954
• Aliases: None
• Description: ribosomal protein L36a-like [Source:HGNC Symbol;Acc:10346]

Sequence

>retro_dnov_227
AGCATTCCCGAAACCCACTGGACTTTCTATAAGAAGTGTGGCAAGGACCAACCCCACAAAGCGATACAGCACAAGAAGGG
TGAGAATTCTCTGTATACCCAGGGAAAGCAGTGTGGTGACAGGAAACAGAGAAGCTATGGAGGACAGACTAAGCCAATTT
TCCAGTAGAAAGCTTAAAACTAAAGAGAGGTTTGTGCTGAGGCTAGAATGTGTTGAGTCCATTTGCAGATATAAGAGAAT
GATGGCTACTGAGAGATGTAAACAATTTGAACTGGGAGGAGATGAGCAGAGAAAGAGCCAAGTGATCCATTTC

Alignment

ORF - retro_dnov_227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.81 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDREQSGYGGQTRPIFREKA-KTTKKIVLRLE
          ..P.T..TF.KKCGK.QPHK..Q.KKG..SLY.QGK...DR.Q..YGGQT.PIF..KA.KT....VLRLE
Retrocopy SIPETHWTFYKKCGKDQPHKAIQHKKGENSLYTQGKQCGDRKQRSYGGQTKPIFQ*KA>KTKERFVLRLE

Parental  CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          CVE..CR.KRM.A..RCK.FELGGD..RK.QVI.F
Retrocopy CVESICRYKRMMATERCKQFELGGDEQRKSQVIHF

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	1.75 RPM	133.99 RPM
SRP012922_cerebellum	0.96 RPM	71.35 RPM
SRP012922_heart	0.46 RPM	65.66 RPM
SRP012922_kidney	0.00 RPM	149.22 RPM
SRP012922_liver	0.46 RPM	64.09 RPM
SRP012922_lung	0.31 RPM	157.00 RPM
SRP012922_quadricep_muscle	0.35 RPM	81.35 RPM
SRP012922_spleen	0.92 RPM	200.65 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_227 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 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015954	23 retrocopies	retro_dnov_1206, retro_dnov_1266, retro_dnov_1320, retro_dnov_1328, retro_dnov_1330, retro_dnov_1392, retro_dnov_1427, retro_dnov_1525, retro_dnov_1799, retro_dnov_1898, retro_dnov_227 , retro_dnov_2302, retro_dnov_233, retro_dnov_2371, retro_dnov_243, retro_dnov_2488, retro_dnov_2503, retro_dnov_2587, retro_dnov_310, retro_dnov_596, retro_dnov_699, retro_dnov_871, retro_dnov_936,
Felis catus	ENSFCAG00000015397	3 retrocopies	retro_fcat_106, retro_fcat_25, retro_fcat_80,
Gorilla gorilla	ENSGGOG00000009460	6 retrocopies	retro_ggor_13, retro_ggor_152, retro_ggor_207, retro_ggor_208, retro_ggor_42, retro_ggor_5,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sorex araneus	ENSSARG00000014178	4 retrocopies	retro_sara_146, retro_sara_488, retro_sara_617, retro_sara_76,
Tursiops truncatus	ENSTTRG00000012779	1 retrocopy	retro_ttru_5,