RetrogeneDB ID: retro_dnov_2594

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_88797:1505..2011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSDNOG00000006966
• Aliases: None
• Description: FGFR1 oncogene partner 2 [Source:HGNC Symbol;Acc:23098]

Sequence

>retro_dnov_2594
AGTTGCACAGTTGTGAAGTCTCTTGCCGATGCTAAAGGTCTTGTTGAAAGATTTTAAGATCACGACGATGTAGCAGAATC
TCTTATTGAGCAAACCACCGCTCTCAACAAGCGAGTAGAAGCCATGAAACAGTATCAGGAAGAAATTCAAGAACTTAATG
AAGTTTCAAGACATTGGCCAAGGTCCACATTAGTCATGGGTATCCAGCAAGAAAATAGACAAATCAGAAAATTGCAGCAA
GAGAATAAAGAATTGCGTCCTCCCTTGAAGAACATCAGTCTGCCGTGGAACTTACAATGAGCAAGTATCGAGAAGAAATG
TTTAGATTGTTAATGGCTAGCAAAAAAGATGATCCAGGTATAATAATGAAGTTAAAAGAGCAGCAGTCTAAAATTGGCAT
GGTACATCATAACAACTCTGAAGGATTCTTTCTTAATGCATCTCGACACATCCTTGAAGCACCTCAACAGGAACTGGAGA
GAAGACACTTGGAAGCAAATCACAAT

Alignment

ORF - retro_dnov_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 66.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SCTIEKALADAKALVERLRDHDDVAESLIEQTTALNKRVEAMKQYQEEIQELNEVARHRPRSTLVMGIQQ
          SCT..K.LADAK.LVER..DHDDVAESLIEQTTALNKRVEAMKQYQEEIQELNEV.RH.PRSTLVMGIQQ
Retrocopy SCTVVKSLADAKGLVERF*DHDDVAESLIEQTTALNKRVEAMKQYQEEIQELNEVSRHWPRSTLVMGIQQ

Parental  ENRQIRELQQENKELR-TSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSKIDMVHRNN
          ENRQIR.LQQENKELR..SLEEHQSA.EL.MSKYRE.MFRLLMASKKDDPGIIMKLKEQ.SKI.MVH.NN
Retrocopy ENRQIRKLQQENKELR<SSLEEHQSAVELTMSKYREEMFRLLMASKKDDPGIIMKLKEQQSKIGMVHHNN

Parental  SEGFFLDASRHILEAPQHGLERRHLEANHN
          SEGFFL.ASRHILEAPQ..LERRHLEANHN
Retrocopy SEGFFLNASRHILEAPQQELERRHLEANHN

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	0.58 RPM	10.11 RPM
SRP012922_cerebellum	0.14 RPM	8.52 RPM
SRP012922_heart	0.00 RPM	1.16 RPM
SRP012922_kidney	0.00 RPM	3.01 RPM
SRP012922_liver	0.00 RPM	3.10 RPM
SRP012922_lung	0.00 RPM	6.72 RPM
SRP012922_quadricep_muscle	0.17 RPM	3.81 RPM
SRP012922_spleen	0.23 RPM	16.37 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_2594 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594 ,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,