RetrogeneDB ID: retro_pabe_3116

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:8346353..8346967(-)
• Located in intron of: None

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_3116
ATGGTAACTGAGATGGTGGAGCTCCATCAGCTGAAGCTTGCTGAACTAAAGCAAGAATGTCTTGCTTGTGGTTTGGAGAC
CAAGGGAATAAAGCAAGATCTTATCCACAGACTCCAGACATATCTTGAAGAACATGCTGAAGAGGAGGCAAATGAAGATG
TACTAGGAGATGAAACAGAAGAAGAAACAAACCCCTTGTCAAATAGGAAGAACCCCCTGAAAAAAACTGTTGATGTGGCA
GCAGAGAAGAAAGTGGTGAAAATTACATCTGAAATACCACAGGCTGAGAGAATGCAGAAGAGGGCCTAACGATTCAGTGT
ACCTGTGAGCTTGGAGGTTAAGAAAGCTGCTCAGGCAGCTAGGTTTGGGATTTCTTCAGTTCCAACAAAAGTCTGTCATC
TGATAACAAACCTATGGTTAACGTGGATAAGCCGAAGGAAAGAGCTCAAAGATTTGGTTTGAATGTCTCTTCAATCTCCA
GAAAGTCTGAAGACGATGAGAAACTGAAAAAGAGGAAGGAGCGATTTGGGATTGTCACAAGTTCAGCTGGAACTGGAACC
ACAGAGGATACAGAGGCAAAGAAGAGGAAAAGAGCAGAGCACTTTGGGATTGCC

Alignment

ORF - retro_pabe_3116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATETVELHKLKLAELKQECLARGLETKGIKQDLIHRLQAYLEEHAEEEANEEDVLGDETEEEET-KPIE
          M.TE.VELH.LKLAELKQECLA.GLETKGIKQDLIHRLQ.YLEEHAEEEANE.DVLGDETE.EET.KP..
Retrocopy MVTEMVELHQLKLAELKQECLACGLETKGIKQDLIHRLQTYLEEHAEEEANE-DVLGDETE-EET<KPL-

Parental  LPVKEEEPPEK-TVDVAAEKKVVKITSEIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTK-GL
          ..VK.EEPPEK.TVDVAAEKKVVKITSEIPQ.ERMQKRA.RF.VPVSLE.KKAA.AARFGISSVPTK..L
Retrocopy --VK*EEPPEK>TVDVAAEKKVVKITSEIPQAERMQKRA*RFSVPVSLEVKKAAQAARFGISSVPTK<SL

Parental  SSDNKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERF
          SSDNKPMVN.DK.KERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAE.F
Retrocopy SSDNKPMVNVDKPKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAEHF

Parental  GIA
          GIA
Retrocopy GIA

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	0.50 RPM	18.63 RPM
SRP007412_cerebellum	1.09 RPM	21.04 RPM
SRP007412_heart	0.36 RPM	16.74 RPM
SRP007412_kidney	0.46 RPM	19.23 RPM
SRP007412_liver	0.15 RPM	11.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3116 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3116 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3882
Pan troglodytes	retro_ptro_2644
Gorilla gorilla	retro_ggor_2613

---

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,