RetrogeneDB ID: retro_pabe_1378

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:28958999..28959836(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000007274
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSPPYG00000002099
• Aliases: None
• Description: Selenide, water dikinase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RF87]

Sequence

>retro_pabe_1378
CCAGCCCTGGGCATCGGGATGGACTCCTGCGTCATCCCCCTGAGGCACGGGGGCCTGTCACTGGTGCAGACCACGGACTT
CTTTTACCCCTTGGTAGAAGATCCCTACATGATGGGGCGCATAGCTTGTGCCAACGTGCTGAGTGACCTCTACGCCATGG
GGATTACTGAGTGTGACAACATGTTGATGTTACTCAGCGTCAGCCAGAGTATGAGTGAGGAGGAACGCGAAAAGGTAACG
CCACTCATGGTCAAAGGCTTTCGGGATGCGGCTGAGGAAGGAGGGACGGCAGTGACCGGTGGGCAAACAGTGGTCAACCC
TTGGATTATAATCGGTGGAGTTGCCACTGTAGTATGCCAGCCAAATGAGTTCATAATGCCGGACAGCGCCGTCGTTGGGG
ACGTGCTGGTGTTAACCAAACCGTTAGGAACCCAGGTTGCTGTCAATGCCCACCAATGGCTGGATAATCCTGAAAGATGG
AATAAAGTAAAGATGGTGGTCTCCAGAGAAGAGGTGGAGCTGGCCTATCAGGAAGCCATGTTCAATATGGCTACCCTCAA
CAGAACTGCTGCAGGTTTAATGCACACATTTAATGCCCATGCGGCCACAGATATCACAGGCTTTGGCATTCTAGGACACT
CCCAGAACCTTGCAAAACAACAAAGAAATGAAGTGTCCTTTGTTATTCATAATCTGCCAATAATTGCCAAGATGGCCGCC
GTCAGCAAGGCCAGTGGACGGTTTGGGCTTCTTCAAGGAACCTCAGCTGAAACCTCTGGGGGATTACTGATTTGTCTGCC
AAGAGAACAGGCGGCTCGCTTTTGTTCTGAAATCAAA

Alignment

ORF - retro_pabe_1378 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.79 %
• Parental protein coverage: 80.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNK
          P.LGIGMD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL.VS..
Retrocopy PALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQS

Parental  MTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTK
          M...ER.KV.PL...GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLVLTK
Retrocopy MSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTK

Parental  PLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGI
          PLGTQVAV..HQWLD.PE.WNK.K.VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFGI
Retrocopy PLGTQVAVNAHQWLDNPERWNKVKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGI

Parental  LGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCGRDK
          LGH.QNLAKQQRNEVSFVIHNLP..AKMAAVSKA.G..FGL..GT..ETSGGLLICLPREQAARFC...K
Retrocopy LGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEIK

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	15.26 RPM	19.85 RPM
SRP007412_cerebellum	19.21 RPM	29.79 RPM
SRP007412_heart	5.45 RPM	8.34 RPM
SRP007412_kidney	42.93 RPM	32.65 RPM
SRP007412_liver	70.26 RPM	17.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1378 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1378 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Felis catus	ENSFCAG00000003921	1 retrocopy	retro_fcat_96,
Macropus eugenii	ENSMEUG00000012188	1 retrocopy	retro_meug_245,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mustela putorius furo	ENSMPUG00000000948	1 retrocopy	retro_mputfur_20,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Pongo abelii	ENSPPYG00000002099	6 retrocopies	retro_pabe_1324, retro_pabe_1378 , retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,