RetrogeneDB ID: retro_dnov_2060

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_45114:9634..10286(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000015545
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSDNOG00000007896
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_dnov_2060
ATGACTGTTGGCAAGAGCAGCAAGATGCTGCAGCACACTGACTACAGGATGAGGTGCATCCTGCAAGACGGCCGTATCTT
CACTGGCACCTTCAAGGCTTTTGACAAGCATATGAACTTGATCCTCTGTGACTGTGATGAGTTCAGGAAGATCAAGCCAA
AGAACTCAAAACAAGCAGAAAGGGAAGAGAAGTATGTCCTTGGACTGGTGCTGCTGCGAGGGGAAAACCTGGTCTCAATG
ACAGTAGAGGGACCTCCTCCCAAAGATACTGGCATTGCCCGAGTGCCACTTGCTGGAGCTGCTGGAGGCCCAGGGATTGG
TAGAGCAGCTGGCAGAGGTATTCCAGCTGGTGTTCCCATGCCCCAGGCTCCTGCAGGACTTGCAGGGCCAGTCCATGGGG
TTGGTGGGCCAACCCAACAGGTAATGACCCCACAGGGAAGAGGCACTGTTGCAGCCGCCGCTGCTGCTGCCACTGCCGCA
GCCAGTATTGCAAGAGCCCCAACCCAGTATCCACCTGGTTCGTGGGGGTCCTCCCCCACCTATGGGCCGAGGAGTACCCC
CTCCAAGCATGATGGGCCCACCTCCTAGAATGAGGCCTCCCATGGGTCCCCCAATGGGGATTCCCCCTGGACGAGGAACT
CCAATGGGCATG

Alignment

ORF - retro_dnov_2060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 74.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVSKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLV
          MTV.KSSKMLQH.DYRMRCILQDGRIF.GTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEK.VLGLV
Retrocopy MTVGKSSKMLQHTDYRMRCILQDGRIFTGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKYVLGLV

Parental  LLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLR-PVRGVGGPSQQ
          LLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGL..PV.GVGGP.QQ
Retrocopy LLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVHGVGGPTQQ

Parental  VMTPQGRGTVAAAAAAAT--ASIAGAPTQYPPG-RGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPP
          VMTPQGRGTVAAAAAAAT..ASIA.APTQYPPG.RGGPPPPMGRG.PPP.MMGPPP.MRPPMGPPMGIPP
Retrocopy VMTPQGRGTVAAAAAAATAAASIARAPTQYPPG>RGGPPPPMGRGVPPPSMMGPPPRMRPPMGPPMGIPP

Parental  GRGTPMGM
          GRGTPMGM
Retrocopy GRGTPMGM

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	14.39 RPM	62.62 RPM
SRP012922_cerebellum	11.96 RPM	98.29 RPM
SRP012922_heart	7.19 RPM	36.20 RPM
SRP012922_kidney	18.07 RPM	78.03 RPM
SRP012922_liver	7.74 RPM	29.72 RPM
SRP012922_lung	18.02 RPM	74.22 RPM
SRP012922_quadricep_muscle	5.19 RPM	41.19 RPM
SRP012922_spleen	15.68 RPM	70.28 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_2060 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 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060 , retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,