RetrogeneDB ID: retro_eeur_434

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_300022:3790..4448(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSEEUG00000015568
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_eeur_434
ATGACCGTGGGCAAGAGCAGCAAGATGCTGCAGCACATCGACTACAGGATGAGGTGCATCCTGCAAGACGGCCACATCTT
CATTGGCACCTTCAAGGCTTTTGACAAGCATTATGAAATTGATCCTGTGTGACTGATGAGTTCAGGAAGATCAAGCCAAA
GAACTCGAAACAAGCAGAAAGAGAAGAAAAACGAGTCCTTGGTCTGGTGCTGCTTCAAGGGGAGAACCTGGTCTCAATGA
CAGTAGAGGGACTCCTCCCTAAGATACTGACATAGCCCGAGTGCCACTGGCTGGAGCTGCTGGAGTCCCAGGTATCGGCA
GGGCTGCTGGCAGAGGAATCCCAGCTGATGTTCCCATGCCACAGGCTCCTGCAGGACTTGCTGGGCCAGTCCGAGGTGTT
GGTGGGCCATCCCAGCAGGTGATGACCCCACAAGGAAGAGGCACCGTTGCTGCTGCTGCAGCTGCTGCCACAGCCAGTAT
TGCGGGAGCTCCAACCCAGTACCCACCGGGCCGTGGAGGTCCTCCCCCACCTATGGGCAGAGGGGCACCCCCTCCCGGCA
TGATGGGCCCACCTCCCGGTATGAGGCCTCCAATGGGTCCCCCAGTGGGGATACCCCCTGGAAGAGGAACTCCAATGGGC
ATGCCCCCTCCAGGAATG

Alignment

ORF - retro_eeur_434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 77.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLI-LCDCDEFRKIKPKNSKQAEREEKRVLGL
          MTVGKSSKMLQHIDYRMRCILQDG.IFIGTFKAFDKH......C..DEFRKIKPKNSKQAEREEKRVLGL
Retrocopy MTVGKSSKMLQHIDYRMRCILQDGHIFIGTFKAFDKHYEID<SCVTDEFRKIKPKNSKQAEREEKRVLGL

Parental  VLLRGENLVSMTVEG-PPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPS
          VLL.GENLVSMTVEG..PP.DT.IARVPLAGAAG.PGIGRAAGRGIPA.VPMPQAPAGLAGPVRGVGGPS
Retrocopy VLLQGENLVSMTVEG<TPP*DTDIARVPLAGAAGVPGIGRAAGRGIPADVPMPQAPAGLAGPVRGVGGPS

Parental  QQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPG
          QQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPP.GIPPG
Retrocopy QQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPVGIPPG

Parental  RGTPMGMPPPGM
          RGTPMGMPPPGM
Retrocopy RGTPMGMPPPGM

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
SRP017611_brain	0.16 RPM	19.82 RPM
SRP017611_kidney	0.38 RPM	47.63 RPM
SRP017611_liver	0.00 RPM	14.95 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_434 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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,