RetrogeneDB ID: retro_pabe_2265

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:163705543..163706095(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSPPYG00000010841
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_pabe_2265
GATGAGTTCAGAAAGATCAAGCCAAAAAACTCCAAACAAGCAGAAAGGGAAGAGAAGCGAATCCTTGGTCTGGTGCTGCT
GCGAGGGGAGAATCTGGTCTCAATGACAGTAGAGGGACCTCCTCCCAAAGATACTGGTATTGCTTGAGTTCCACTTGCTG
GAACTGCCGGGGACCCAGGGATCGGCAGGGCTGCTGGCAGAGGAATCCCAGCTGGGGTTCCCATGCCCCAGGCTCCTGCA
GGACTTGCTGGGCCAGTCCGTGGGGTTGGCTGGCCATCCCAAAAGGTGATGACCCTACAAGAAAGAGGTACTGTTGCAGC
CACTGCAGCTGCTGCCACAGCCAGTATTGCCGGGGCCCCGACCCAGTACCCACCTGGCCGTGGGGGTCCTCCCCAACCTA
TGGGCCAAGGAGCACCCCCTCCAGGCATGATGGGCCCACCTCCTGGTATGAGGCCTCCTATGGGTCCCCCAGTGGGGATC
ACCCCTGGAAGAGGGACTCCAATGGGCATGCCCCCTCCGGGAATGCGGCCTCCTCCCCCTGGGATGCAAGGG

Alignment

ORF - retro_pabe_2265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.39 %
• Parental protein coverage: 79.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIP
          DEFRKIKPKNSKQAEREEKR.LGLVLLRGENLVSMTVEGPPPKDTGIA.VPLAG.AG.PGIGRAAGRGIP
Retrocopy DEFRKIKPKNSKQAEREEKRILGLVLLRGENLVSMTVEGPPPKDTGIA*VPLAGTAGDPGIGRAAGRGIP

Parental  AGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPP
          AGVPMPQAPAGLAGPVRGVG.PSQ.VMT.Q.RGTVAA.AAAATASIAGAPTQYPPGRGGPP.PMG.GAPP
Retrocopy AGVPMPQAPAGLAGPVRGVGWPSQKVMTLQERGTVAATAAAATASIAGAPTQYPPGRGGPPQPMGQGAPP

Parental  PGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRG
          PGMMGPPPGMRPPMGPP.GI.PGRGTPMGMPPPGMRPPPPGM.G
Retrocopy PGMMGPPPGMRPPMGPPVGITPGRGTPMGMPPPGMRPPPPGMQG

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
SRP007412_brain_prefrontal_cortex	0.06 RPM	17.69 RPM
SRP007412_cerebellum	0.73 RPM	25.05 RPM
SRP007412_heart	0.03 RPM	10.14 RPM
SRP007412_kidney	0.07 RPM	24.56 RPM
SRP007412_liver	0.15 RPM	19.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2265 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2265 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 34 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	ENSPPYG00000006269	1 retrocopy	retro_pabe_1900,
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,