RetrogeneDB ID: retro_pabe_1108

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:50083908..50084533(+)
• Located in intron of: ENSPPYG00000005791

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK16
• Ensembl ID: ENSPPYG00000013202
• Aliases: None
• Description: serine/threonine kinase 16 [Source:HGNC Symbol;Acc:11394]

Sequence

>retro_pabe_1108
ATGGGCCATGCACTGTGTGCCTGCTCTTAGGGAAATGTCATCATTGACAATAGCTATTTCTTCATCCAGAAGCTGGGGGA
GAGTGGGTTCAGCTATGTGGACCTAGTGGAGGGGTTACAGGATGGACACTTCTACGCCCTGAAGTGAATCCTGTGTCACG
AGCAGCAGGACCGGGAGGAGGCCCAGCCAAGAAGCAAACATGCATCACCTCTTCAATCACCCCAACATCCTTTACCTCAC
AGCTTACTGTCTGAGGGAGTAGGGTGCTAAGCATGAGGCCTGGCTGCTGCTTCTGTTCTTTAAGAGAGGTATACTGTGGA
ATGGAGAGAAAGGCCGAAGGACGATGGCAACTTCCTGACTTAGGATCAAATCCTTCAGCTCCTGCTGGGTATCTACAGCA
GCTTGAGGCCATTCATGCCAAGGGTTAGGCCCACAGGGACCTGAAGCCCACCACTATCTTGCTTGGAGACGAGGGGCAGC
CAGTTTTAATACACTTGGATGCCATGAATCAAGCATGCCTCACATGAAGGGCTCCCACCAGGCCCTGACCCTGCAGGACT
AGGCGACCCAGCAGTGCACCATCTCCTACTGAGCCCTAGAGCTCTTCCCTGAGCAGTCACTGTGT

Alignment

ORF - retro_pabe_1108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 68.85 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGHALCVCSRGTVIIDNKRYLFIQKLGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQ-READMH
          MGHALC.CS.G.VIIDN..Y.FIQKLGE.GFSYVDLVEGL.DGHFYALK.ILCHEQQDREEAQ..EA.MH
Retrocopy MGHALCACS*GNVIIDNS-YFFIQKLGESGFSYVDLVEGLQDGHFYALK*ILCHEQQDREEAQ>QEANMH

Parental  RLFNHPNILRLVAYCLRERGAKHEAWLLLPFFKRGTLWNE-IERLKDKGNFLTEDQILWLLLGI-CRGLE
          .LFNHPNIL.L.AYCLRE.GAKHEAWLLL.FFKRG.LWN...ER.KD.GNFLT.DQIL.LLLGI....LE
Retrocopy HLFNHPNILYLTAYCLRE*GAKHEAWLLLLFFKRGILWNG<RERPKDDGNFLT*DQILQLLLGI<LQQLE

Parental  AIHAKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACI-HVEGSRQALTLQDWAAQRCTISYRAPELFSV
          AIHAKG.AHRDLKPT.ILLGDEGQPVL..L..MNQAC..H..GS.QALTLQD.A.Q.CTISY.A.ELF..
Retrocopy AIHAKG*AHRDLKPTTILLGDEGQPVLIHLDAMNQACL<HMKGSHQALTLQD*ATQQCTISY*ALELFPE

Parental  QSHC
          QS.C
Retrocopy QSLC

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	30.63 RPM
SRP007412_cerebellum	0.00 RPM	10.82 RPM
SRP007412_heart	0.00 RPM	5.60 RPM
SRP007412_kidney	0.00 RPM	29.83 RPM
SRP007412_liver	0.00 RPM	19.95 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1108 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1108 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1334
Pan troglodytes	retro_ptro_911
Gorilla gorilla	retro_ggor_1040

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000152	1 retrocopy	retro_dord_692,
Equus caballus	ENSECAG00000014093	1 retrocopy	retro_ecab_166,
Homo sapiens	ENSG00000115661	1 retrocopy	retro_hsap_1334,
Gorilla gorilla	ENSGGOG00000010907	1 retrocopy	retro_ggor_1040,
Macropus eugenii	ENSMEUG00000006422	1 retrocopy	retro_meug_1579,
Myotis lucifugus	ENSMLUG00000008066	1 retrocopy	retro_mluc_1213,
Pongo abelii	ENSPPYG00000013202	1 retrocopy	retro_pabe_1108 ,
Pan troglodytes	ENSPTRG00000012948	1 retrocopy	retro_ptro_911,
Ictidomys tridecemlineatus	ENSSTOG00000025197	2 retrocopies	retro_itri_1662, retro_itri_602,