RetrogeneDB ID: retro_pabe_3431

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:90454024..90454558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPS2
• Ensembl ID: ENSPPYG00000020125
• Aliases: None
• Description: Ribose-phosphate pyrophosphokinase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R8F8]

Sequence

>retro_pabe_3431
ATGCCCAACATCGTGCTGTTCAGCGGCAGCTCGCACCAGGACCTGTCCCAGCGCGTGGCCCACCGCCTGGGCCTGGAGCT
GGGCAAGGTGGTCACCAAGAAGTTCAGCAACCAGGAGACCAGCGTGGAAATTGGTGACAGTGTGAGAGAGGAAGATGTCT
ACATCATCCAGAGCGGCTGGGGGGAAATTAACAACAACCTGATGGAGCTCCTCATCATGATCAATGCCTGCAGGATTTCG
TCATCATCCAGGGTGACTGCTGTGATCCCGTGTTTCCCATACGCCCGACAAGACAAAAAGGACAAGAGTCACGCCCCAAT
TTCTGCAAAACTTATGGCCAATATGCTGTCGGTGGCTGGGGCGGATCACATCATCACCATGGACCTACATGTCTCTCAGG
TACAGGGATTCTTTGATATTCCTGTGGATAATTTGTATGCGGAGCCCGCAGTCCTGCAGTGGATTCCGGAAAACATTGCG
GAGTGGAAGAACTGTATCATTGTTTCACCTGAGCCAAAAGGGTCACGTCAATTG

Alignment

ORF - retro_pabe_3431 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.2 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPNIVLFSGSSHQDLSQRVA.RLGLELGKVVTKKFSNQETSVEIG.SVR.EDVYIIQSG.GEIN.NLMEL
Retrocopy MPNIVLFSGSSHQDLSQRVAHRLGLELGKVVTKKFSNQETSVEIGDSVREEDVYIIQSGWGEINNNLMEL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKKDKSRAPISAKLVA-MLSV-GADHIITMDLHASQIQGFFDI
          LIMINAC.I.SSSRVTAVIPCFPYARQDKKDKS.APISAKL.A.MLSV.GADHIITMDLH.SQ.QGFFDI
Retrocopy LIMINACRISSSSRVTAVIPCFPYARQDKKDKSHAPISAKLMANMLSVAGADHIITMDLHVSQVQGFFDI

Parental  PVDNLYAEPAVLQWIRENIAEWKNCIIVSPDAGGAKRV
          PVDNLYAEPAVLQWI.ENIAEWKNCIIVSP...G....
Retrocopy PVDNLYAEPAVLQWIPENIAEWKNCIIVSPEPKGSRQL

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	0.55 RPM	16.48 RPM
SRP007412_cerebellum	0.49 RPM	6.08 RPM
SRP007412_heart	0.06 RPM	2.86 RPM
SRP007412_kidney	0.36 RPM	28.21 RPM
SRP007412_liver	0.09 RPM	9.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3431 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3431 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011662	2 retrocopies	retro_cfam_1037, retro_cfam_1433,
Callithrix jacchus	ENSCJAG00000003885	1 retrocopy	retro_cjac_364,
Echinops telfairi	ENSETEG00000005166	2 retrocopies	retro_etel_1613, retro_etel_669,
Felis catus	ENSFCAG00000026323	1 retrocopy	retro_fcat_527,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323, retro_mdom_1359, retro_mdom_258, retro_mdom_834,
Otolemur garnettii	ENSOGAG00000016087	1 retrocopy	retro_ogar_1440,
Procavia capensis	ENSPCAG00000001197	2 retrocopies	retro_pcap_219, retro_pcap_292,
Pongo abelii	ENSPPYG00000020125	1 retrocopy	retro_pabe_3431 ,
Pongo abelii	ENSPPYG00000020612	2 retrocopies	retro_pabe_3061, retro_pabe_46,
Pteropus vampyrus	ENSPVAG00000009452	1 retrocopy	retro_pvam_1224,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,
Ictidomys tridecemlineatus	ENSSTOG00000006056	1 retrocopy	retro_itri_1668,
Tupaia belangeri	ENSTBEG00000009917	1 retrocopy	retro_tbel_1245,
Tursiops truncatus	ENSTTRG00000003226	1 retrocopy	retro_ttru_1494,