RetrogeneDB ID: retro_pabe_3358

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:108064447..108064964(-)
• Located in intron of: ENSPPYG00000018794

Retrocopy information

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

Parental gene information

• Parental gene symbol: SARNP
• Ensembl ID: ENSPPYG00000004630
• Aliases: SARNP, CIP29, HCC1
• Description: SAP domain-containing ribonucleoprotein [Source:UniProtKB/Swiss-Prot;Acc:Q5R4V4]

Sequence

>retro_pabe_3358
CTCCAGGCATATCTTTCAGGGCATGCTGAAGAGGCAAATGAAGAAGTACTGGGAGATGAAACAGAGAAAGAAGAAACAAA
GCCCCATAGAAATCCCTGTCAAAGAGGAAGAACTCCCTGAAAAAACTGTTGATGTGGAAGCAGAGAAGAAAGTGGTAAAA
ATTACATCTGAAATACCACAGGCGGAGAGAACGCAGAAGAGGGCTGAACGAGTCCATGTACCTGTGAGCCTGTAAAGTAA
GAAAACTGCCCAGGCAGCTAGGTTTGGGACTTCTTCAGTTTCAACAAAAGGTCTGCCATCTAACAACAAACCTATCATGA
ACCTGGATAAGCTAAAGGAAAGAGCTCAAAGATTTGGTTTGAATGGCTCTTCAATCTCCATAAAGTCTGAAGATGGTGAG
AAACTGAAAAGGAGGAAGGAGCGATTTGGAATTATCACCGGTTCAGCTGGAACCGGAAGGAACACAGAGGATACAGAGGC
AAAGAATAGGAAAAGAGCCGCATGCTGTGGGATTGCC

Alignment

ORF - retro_pabe_3358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.57 %
• Parental protein coverage: 82.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQAYLEEHAEEEANEEDVLGDETEEEETKP-IELPVKEEEPPEKTVDVAAEKKVVKITSEIPQTERMQKR
          LQAYL..HAEE.ANEE.VLGDETE.EETKP.IE.PVKEEE.PEKTVDV.AEKKVVKITSEIPQ.ER.QKR
Retrocopy LQAYLSGHAEE-ANEE-VLGDETEKEETKP>IEIPVKEEELPEKTVDVEAEKKVVKITSEIPQAERTQKR

Parental  AERFNVPVSLESKKAARAARFGISSVPTKGLSSDNKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKK
          AER..VPVSL.SKK.A.AARFG.SSV.TKGL.S.NKP..NLDKLKERAQRFGLN.SSIS.KSED.EKLK.
Retrocopy AERVHVPVSL*SKKTAQAARFGTSSVSTKGLPSNNKPIMNLDKLKERAQRFGLNGSSISIKSEDGEKLKR

Parental  RKERFGIVTSSAGTG-TTEDTEAKKRKRAERFGIA
          RKERFGI.T.SAGTG..TEDTEAK.RKRA...GIA
Retrocopy RKERFGIITGSAGTGRNTEDTEAKNRKRAACCGIA

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	0.00 RPM	18.63 RPM
SRP007412_cerebellum	0.00 RPM	21.04 RPM
SRP007412_heart	0.00 RPM	16.74 RPM
SRP007412_kidney	0.00 RPM	19.23 RPM
SRP007412_liver	0.00 RPM	11.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3358 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3358 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2782
Callithrix jacchus	retro_cjac_1487

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011769	2 retrocopies	retro_amel_1602, retro_amel_347,
Bos taurus	ENSBTAG00000020662	1 retrocopy	retro_btau_202,
Callithrix jacchus	ENSCJAG00000007853	8 retrocopies	retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus	ENSCPOG00000011755	1 retrocopy	retro_cpor_1313,
Dipodomys ordii	ENSDORG00000001065	1 retrocopy	retro_dord_80,
Erinaceus europaeus	ENSEEUG00000015176	1 retrocopy	retro_eeur_549,
Homo sapiens	ENSG00000205323	1 retrocopy	retro_hsap_3882,
Gorilla gorilla	ENSGGOG00000013217	2 retrocopies	retro_ggor_2613, retro_ggor_2753,
Loxodonta africana	ENSLAFG00000015053	1 retrocopy	retro_lafr_1024,
Microcebus murinus	ENSMICG00000010902	1 retrocopy	retro_mmur_358,
Monodelphis domestica	ENSMODG00000028949	1 retrocopy	retro_mdom_1909,
Mustela putorius furo	ENSMPUG00000000885	1 retrocopy	retro_mputfur_617,
Mus musculus	ENSMUSG00000078427	1 retrocopy	retro_mmus_54,
Nomascus leucogenys	ENSNLEG00000017599	2 retrocopies	retro_nleu_2779, retro_nleu_569,
Procavia capensis	ENSPCAG00000009477	2 retrocopies	retro_pcap_262, retro_pcap_45,
Pongo abelii	ENSPPYG00000004630	2 retrocopies	retro_pabe_3116, retro_pabe_3358 ,
Pan troglodytes	ENSPTRG00000029747	2 retrocopies	retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus	ENSRNOG00000030520	2 retrocopies	retro_rnor_1326, retro_rnor_471,