RetrogeneDB ID: retro_ptro_911

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:48580159..48580784(+)
• Located in intron of: ENSPTRG00000006319

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK16
• Ensembl ID: ENSPTRG00000012948
• Aliases: None
• Description: None

Sequence

>retro_ptro_911
ATGGGCCATGCACTGTGTGCCTGCTCTTAGGGAAATGTCATCATTGACAATAGCTATTTCTTCATCCAGAACCTGGGGGA
GAGTGGGTTCAGCCATGTGGACCTAGTGGAGGGGTTACAGGATGGACACTTCTATGCCCTGAAGCGAATCCTGTGTCACG
AGCAGCAGGACTGGGAGGAGGCCCAGCCAAGAAGCGAACATGCATCACCTCTTCAATCACCCCAACATCCTTTACCTCAC
GGCTTACTGTCTGAGGGAGTAGGGTGCTAAGCATGAGGCCCAGCTGCTGCTTCCGTTCTTTAAGAGAGATATACTGTGGA
ATGGAGAGAAAGGCCGAAGGACGATGGCAACTTCCTGACTTAGGATCAAATCCTTCAGCTCCTGCTGGGTATCTACAGCG
GCTTGAGGCCATTCATGCCAAGGGTTAGGCCCACAGGGACCTGAAGCCCACCACTATCTTGCTTGGAGACGAGGGGCAGC
CAGTTTTAATACACTTGGATGCCATGAATCAAGCATGCCTCACATGAAGGGCTCCCACCAGGCCCTGACCCTGCCGGACT
AGGCGACCCAGCAGTGCACCATCTCCTACTGAGCCCTAGAGCTCTTCCCTGAGCAGTCACTGTGT

Alignment

ORF - retro_ptro_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.7 %
• Parental protein coverage: 68.85 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGHALCVCSRGTVIIDNKRYLFIQKLGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQ-READMH
          MGHALC.CS.G.VIIDN..Y.FIQ.LGE.GFS.VDLVEGL.DGHFYALKRILCHEQQD.EEAQ..EA.MH
Retrocopy MGHALCACS*GNVIIDNS-YFFIQNLGESGFSHVDLVEGLQDGHFYALKRILCHEQQDWEEAQ>QEANMH

Parental  RLFNHPNILRLVAYCLRERGAKHEAWLLLPFFKRGTLWNE-IERLKDKGNFLTEDQILWLLLGICRG-LE
          .LFNHPNIL.L.AYCLRE.GAKHEA.LLLPFFKR..LWN...ER.KD.GNFLT.DQIL.LLLGI..G.LE
Retrocopy HLFNHPNILYLTAYCLRE*GAKHEAQLLLPFFKRDILWNG<RERPKDDGNFLT*DQILQLLLGIYSG<LE

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

Parental  PSHC
          .S.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	0.04 RPM	20.32 RPM
SRP007412_cerebellum	0.22 RPM	10.97 RPM
SRP007412_heart	0.03 RPM	8.74 RPM
SRP007412_kidney	0.05 RPM	42.05 RPM
SRP007412_liver	0.03 RPM	27.10 RPM
SRP007412_testis	0.00 RPM	51.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_911 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_911 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1334
Gorilla gorilla	retro_ggor_1040
Pongo abelii	retro_pabe_1108

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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,