RetrogeneDB ID: retro_pabe_2620

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:15818999..15819832(+)
• Located in intron of: None

Retrocopy information

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

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_2620
GGCCCAGCCCTTCCAGCCCTGGGCATTGGGCTAGACTCTTGCATCATCTCACTGAGGCATGGAGGCCTGTCACTGGTGCA
GACCATGGACTTCTGTTACTCCTTGGTGGAGGATCCCTACATGAAGGGGTGCATAGCTTGTGCCAATGCGCTGAGTGACC
TCTAGGCCATAGGCATTACTGAGTGTGACAACGTGTTGACGTTACTCAGCTGTTGCCAGAGTATGAGTGAGGAGGAACGC
GAAAAGATAATGCCACTCATGATCAAAGGCTTTCGGGACGCTACTGAGGAGGGAGGAACTGCAGTGACAGGTGGACAAAT
GGTGGTCAACTCTTGGCTTATCATCAGTGGAGTTGCCTCTGTGGTGTGTCGGCCAAGTGCATTCATAATGCCTGATAATG
CGGCTGTTGGGGATGTGCTGGTGTTAACCAAACCCTTAGGAACCCAAGTTGCTGTCAACGCCCACCAATGGCTGGATAAT
ACTGAAAGATGGAATCAGGTGAAGATGGTGGTCTTCAGAGAAGAAGTAGATCTGGCCTATCAGGAAGCTATGCTCAATAT
GGCTACCGTCAACAGAACTGCTGCTAGATTAATGCACAAATTTAATGCCCATGTGGCCACAGACATCACAGGCTTTGGCA
TTCTAGGACACTCTCAGAACCTCGTGAAGCAACAAAGAAATGATGGGTCCTTTATCATTTGCAATCTGCCAGTCATTGCC
AAGATGGCTGCCATCGGCAAGGCCAGTGGGCAGTTTGGGCTTCTTCAAGGAACCTCAGCTGAAACCTCAGGATATTACTG
ATTTGTCTTCCAAGAGAACAGGTGGCTCACTTT

Alignment

ORF - retro_pabe_2620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 80.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAVMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLG
          G...P.LGIG.D.C.I.LRHGGLSLVQT.D..Y..V.DPYM.G.IACAN.LSDL.A.G.TECDN.L.LL.
Retrocopy GPALPALGIGLDSCIISLRHGGLSLVQTMDFCYSLVEDPYMKGCIACANALSDL*AIGITECDNVLTLLS

Parental  VSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVL
          ....M...ER.K.MPL.I.GF.DA.EE.GT.VTGGQ.V.N.W....GVA..VC.P..FIMPDNA..GDVL
Retrocopy CCQSMSEEEREKIMPLMIKGFRDATEEGGTAVTGGQMVVNSWLIISGVASVVCRPSAFIMPDNAAVGDVL

Parental  VLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDIT
          VLTKPLGTQVAV..HQWLD..E.WN..K.VV..E.V.LAYQEAM.NMA..NRTAA.LMH.FNAH.ATDIT
Retrocopy VLTKPLGTQVAVNAHQWLDNTERWNQVKMVVFREEVDLAYQEAMLNMATVNRTAARLMHKFNAHVATDIT

Parental  GFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGG-LLICLPREQAARF
          GFGILGH.QNL.KQQRN..SF.I.NLPV.AKMAA..KA.G..FGL..GT..ETSG..LLICLPREQ.A.F
Retrocopy GFGILGHSQNLVKQQRNDGSFIICNLPVIAKMAAIGKASG-QFGLLQGTSAETSGY<LLICLPREQVAHF

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	19.85 RPM
SRP007412_cerebellum	0.00 RPM	29.79 RPM
SRP007412_heart	0.00 RPM	8.34 RPM
SRP007412_kidney	0.00 RPM	32.65 RPM
SRP007412_liver	0.00 RPM	17.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2620 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2620 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2620 has 0 orthologous retrocopies within eutheria group .

---

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,