RetrogeneDB ID: retro_dnov_261

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_31:17743..18009(-)
• Located in intron of: ENSDNOG00000015661

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX24
• Ensembl ID: ENSDNOG00000019810
• Aliases: None
• Description: sorting nexin 24 [Source:HGNC Symbol;Acc:21533]

Sequence

>retro_dnov_261
TTGGGAACACATTTACAGTCTGTCATTTTAGAAAATGAAAATCTCCCCAAACTGTTTCTTGATTTCCTAATGTGTGACAC
TTGCCCTCTTTTGCCAAAGGCAAAGAGTTGTGGATCTTTTGATAAGACAGAATCTGAAGAGTGAAGCAAACTCCCACAAG
CTGGTGTAACTGTCCTCTGGGATCCATTATCTTGCCTACAGCCAGCAATTTGCCAAATGTGGTTTTTGAAGGAGTTCTCC
ATGGGGTAGTTTACCCTCGTTTGCAG

Alignment

ORF - retro_dnov_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.82 %
• Parental protein coverage: 50.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LETYLQAVILENEELPKLFLDFL-NVRHLPS-LPKAESCGSFDETESEESSKLSHQPVLLFLRDP-YVLP
          L.T.LQ.VILENE.LPKLFLDFL.NV.HLPS.LPKA.SCGSFD.TESEE.SKL....V...L.DP...LP
Retrocopy LGTHLQSVILENENLPKLFLDFL<NV*HLPS>LPKAKSCGSFDKTESEE*SKLPQAGVTV-LWDP<IILP

Parental  TASDFPSVVIEGVLHGIFYSHLQ
          TAS..P.VV.EGVLHG..Y..LQ
Retrocopy TASNLPNVVFEGVLHGVVYPRLQ

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	2.14 RPM
SRP012922_cerebellum	0.27 RPM	8.80 RPM
SRP012922_heart	0.00 RPM	11.37 RPM
SRP012922_kidney	0.00 RPM	13.14 RPM
SRP012922_liver	0.15 RPM	3.87 RPM
SRP012922_lung	0.15 RPM	8.55 RPM
SRP012922_quadricep_muscle	0.00 RPM	18.87 RPM
SRP012922_spleen	0.46 RPM	17.97 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_261 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031069	1 retrocopy	retro_btau_640,
Choloepus hoffmanni	ENSCHOG00000006859	2 retrocopies	retro_chof_1841, retro_chof_544,
Dasypus novemcinctus	ENSDNOG00000019810	1 retrocopy	retro_dnov_261 ,
Echinops telfairi	ENSETEG00000010310	1 retrocopy	retro_etel_923,
Microcebus murinus	ENSMICG00000001708	1 retrocopy	retro_mmur_1043,
Myotis lucifugus	ENSMLUG00000009392	2 retrocopies	retro_mluc_1022, retro_mluc_2330,
Monodelphis domestica	ENSMODG00000013427	1 retrocopy	retro_mdom_1215,
Otolemur garnettii	ENSOGAG00000005170	2 retrocopies	retro_ogar_2940, retro_ogar_975,
Sorex araneus	ENSSARG00000009785	1 retrocopy	retro_sara_99,
Sarcophilus harrisii	ENSSHAG00000011329	1 retrocopy	retro_shar_488,
Tarsius syrichta	ENSTSYG00000014395	2 retrocopies	retro_tsyr_1563, retro_tsyr_1691,