RetrogeneDB ID: retro_dnov_443

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4761:134594..135236(+)
• Located in intron of: ENSDNOG00000004477

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSDNOG00000013904
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:HGNC Symbol;Acc:25930]

Sequence

>retro_dnov_443
CAAGATGGGAATAGCATCCATGGCACCACCCCTCAATATCTGGTGGAGAAGATCATTCAGGCATGAGTCTATGAGTCCAA
GTACTGGAGAGAGGGTATCTTGGACTTACTGCTAAGCTAGTAGTTGATAAAGCCATGGAGTTAAGATTTGTAGATGGCGT
CCATGGAGACAGCATAAAGCCAACTCCCCATTCTGTGCTTGACCTTGAAGATGTTGCACATTCAACCCAAGAAGGATACC
ACTGTAGGGTTTATCAAAAATGAACATTTTGAGTATGTTCACATGTTGGGGGCACTTTGCATGAGGCTGATGGGCACTGC
AATTGATTGCTGCGAGTCCTTGGAACCTCTGTACAATGACTCTTAGAAAATCAAGAGCCAGAAACGAAATGGGAAGCTTG
AACAGATGCACGTGGATGAGTGTGACGAGCTGCTGCACCGTGAGAGATGGGTGACATCAGTCTGTGCCGGCTGCAGCAAC
GTAGTGTGTTGGACGAAGCGGAGCCCCTGGAGCCTCAGGTTAGTGCCCTAGAAGAGGACGTGGATGGTGGGGCCCAGCGA
AGGAGAGGAGGAGGACGAGCAGGCAGAGGGAGTGCCATCACCCGATCACCACCCACGACGCGACCGCGACATGGACAAGC
CC

Alignment

ORF - retro_dnov_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.78 %
• Parental protein coverage: 69.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDAHSIHGTNPQYLVEKIIRTRIYESKYWKEECF-GLTAELVVDKAMELRFVGGVYGGNIKPTP-FLCLT
          .D..SIHGT.PQYLVEKII....YESKYW.E....GLTA.LVVDKAMELRFV.GV.G..IKPTP..LCLT
Retrocopy QDGNSIHGTTPQYLVEKIIQA*VYESKYWREGIL<GLTAKLVVDKAMELRFVDGVHGDSIKPTP>ILCLT

Parental  LKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHV
          LKML.IQP.KD..V.FIKNE.F.YV.MLGAL.MRL.GTAIDC...LEPLYND..KIKSQ.RNG..E.MHV
Retrocopy LKMLHIQPKKDTTVGFIKNEHFEYVHMLGALCMRLMGTAIDCCESLEPLYNDS*KIKSQKRNGKLEQMHV

Parental  DEFIDELLHSER-VCDIILPRLQKRYVLEEAEQLEPRVSALEEDMDD-VESSEEEEEEDEKLERVPSPDH
          DE..DELLH.ER...DI.L.RLQ.R.VL.EAE.LEP.VSALEED.D....S..EEE..DE..E.VPSPDH
Retrocopy DE-CDELLHRER<MGDISLCRLQQRSVLDEAEPLEPQVSALEEDVDG>GPSEGEEE--DEQAEGVPSPDH

Parental  RRRSYRDLDKP
          ..R..RD.DKP
Retrocopy HPRRDRDMDKP

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	13.03 RPM
SRP012922_cerebellum	0.00 RPM	10.31 RPM
SRP012922_heart	0.00 RPM	3.48 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	6.19 RPM
SRP012922_lung	0.15 RPM	15.27 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.33 RPM
SRP012922_spleen	0.00 RPM	18.08 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_443 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 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443 ,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,