RetrogeneDB ID: retro_pabe_3115

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:7883292..7884298(-)
• Located in intron of: ENSPPYG00000017366

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF14
• Ensembl ID: ENSPPYG00000015894
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF14 [Source:RefSeq peptide;Acc:NP_001125890]

Sequence

>retro_pabe_3115
ATGTTGTCAGAAGACTGAGAAGCTCAGGAGGTGAACTGCTGGCCCTGGCGAGTATTATCATGGAGATGAATTCAGAAAAG
CAGAGCCTGTCCGAGGTGGAGAAATCAGGATCGATTTGGATTTGCCACAGAACTTCAAGATATTTGTGAGCGGCAGTTCA
GATGAGTGCCCCCAGAAGAGTGGCTTTGAGTATACATTTGCTTTCTCCCTCCAGTTGTGCTGAACTCTGAACTGCCACCA
GAATATCCATCCTCCTTCCCACCTTCATTCACACTCAGTGGCAAATTGCTGCCACCAACTCAGCTCTCTGCTCTATGTAA
GTACTTAGACAACCTATGGGAAGGACACAGTGGCAGCGGGATCCTGTCTGCTGGATGCAGTTTCTTAAGCAAGAGGCCCT
GGTGCATCCGAATATTGTCTCTCCCACTGAGCTCAAGATGGGTTCTCAGGAAGAAGTGCTGAGAAGGACAGCTCAAGCCT
CTCCCATCACAGAGCTAGATTTTGGAGGAGCTGCTGGATCTCATGTAGACCAAGAGGAAACTGTGGGTGATAGAGCTGTG
CAGGATGTGGAAGTAGAATCACTGTCAAGTCTGATCCAGGAAATCTTGGACTTTGATCAAGCTCAGCAGATAAAATGCTT
TAATAGTAGATTGTTCCTGTACGACATCTGTTTCTTTGAGAAGCTGGGCAGTGAATGCATGTACTTCTTGGAGTGAGGCC
TGTGTACTGCAAAGCCTGTCTGAAGGACTGCTTTGAAATCCAGATCAGAGATGGCCAGGTTCAATGCCTCAACTGCTCAG
AACCAAAGTGCCCTTCGGTGGCCACTCCTGGCCAGGTCAAAGAGCCAGTGGAAGCAGAGTTATCTGCCCGTCATGGCTGC
CTTCTCCTCCCATCCACCTTGGAGCTGGTGGCAGATGTGGTGTGCTGCCCCCGCCTGTGGGGGCCTGCAGGGCCTAGCTG
TACCATGGGCATCTGCTCCAGCTGCAACTTTGCCTTCTGTACCTTG

Alignment

ORF - retro_pabe_3115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.75 %
• Parental protein coverage: 71.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSSEDREAQE-DELLALASI-YDGDEFRKAESVQGGETRIYLDLPQNFKIFVSGNSNECLQNSGFEYT-I
          M.SED.EAQE..ELLALASI.Y.GDEFRKAE.V.GGE.RI.LDLPQNFKIFVSG.S.EC.Q.SGFEYT.I
Retrocopy MLSED*EAQE<GELLALASI<YHGDEFRKAEPVRGGEIRIDLDLPQNFKIFVSGSSDECPQKSGFEYT<I

Parental  CFLPPLVLNFELPPDYPSSSPPSFTLSGKWLSPTQLSALCKHLDNLWEEHRGSVVLFA-WMQFLKEETLA
          CFLPP.VLN.ELPP.YPSS.PPSFTLSGK.L.PTQLSALCK.LDNLWE.H.GS..L.A.WMQFLK.E.L.
Retrocopy CFLPPVVLNSELPPEYPSSFPPSFTLSGKLLPPTQLSALCKYLDNLWEGHSGSGILSA<WMQFLKQEALV

Parental  YLNIVSPFELKIGSQKKVQRRTAQASPNTELDFGGAAGSNVDQEEIVDERAVQDVE--SLSNLIQEILDF
          ..NIVSP.ELK.GSQ..V.RRTAQASP.TELDFGGAAGS.VDQEE.V..RAVQDVE..SLS.LIQEILDF
Retrocopy HPNIVSPTELKMGSQEEVLRRTAQASPITELDFGGAAGSHVDQEETVGDRAVQDVEVESLSSLIQEILDF

Parental  DQAQQIKCFNSKLFLCNICFCEKLGSECMYFLE-CRHVYCKACLKDYFEIQIRDGQVQCLNCPEPKCPSV
          DQAQQIKCFNS.LFL..ICF.EKLGSECMYFLE..R.VYCKACLKD.FEIQIRDGQVQCLNC.EPKCPSV
Retrocopy DQAQQIKCFNSRLFLYDICFFEKLGSECMYFLE<VRPVYCKACLKDCFEIQIRDGQVQCLNCSEPKCPSV

Parental  ATPGQVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQLPVMQEPGCTMGICSSCNFAFCTL
          ATPGQVKE.VEAEL.AR...LLL.S.L.L.AD.V.C...C..L.....P.CTMGICSSCNFAFCTL
Retrocopy ATPGQVKEPVEAELSARHGCLLLPSTLELVAD-VVC---CPRLWGPAGPSCTMGICSSCNFAFCTL

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	46.00 RPM
SRP007412_cerebellum	0.73 RPM	43.78 RPM
SRP007412_heart	0.09 RPM	35.64 RPM
SRP007412_kidney	0.00 RPM	41.20 RPM
SRP007412_liver	0.03 RPM	29.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3115 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3115 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3881
Pan troglodytes	retro_ptro_2643
Gorilla gorilla	retro_ggor_2612

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115 ,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571, retro_ptro_2643,