RetrogeneDB ID: retro_pabe_3095

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:132255299..132256169(+)
• Located in intron of: None

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_3095
GACAGCTGTGTGGAGGATGTGGAATCATTGTTAAATATGATCCAGGAAATCTTGGACTTTGATCAAGCTCAGCAGATAAA
ATGCTTTAATAGTAATTTGTTCCTGTGCAATATCTGTTTCTGTAAGAAGCTGGGTAGTGAATGCATGTACTTCTTGGAGT
GCACGCATGTGTACTGCAAAGCCTGTCTGAAGGACTACTTTGAAATCCAGATCAGAGATGGCCAGGTTCAATGTCTCAAC
TGCCCAGAACCAAAGTGCCCTTCAGTGGCCACTCCTGGTCAGGTCAAAGAGCTAGTGGAAGCAGAATTATTTGCCCATTA
TGACTGCCTTCTCCTCCAGTCCACCTTGGACCTGATGGCAGATGTGGTGTACTGCCCCCACCCGTGCTGCCAGCTGCCTG
TGATGCAGGAGCCTGGCTGCACCGTGGGTATCTGCTCTAGCTGCAATTTTGCCTTCTGTACCTTGTGCAGGTTGACCTAC
CATGGGGTCTCTCCATGTAAGGTGACTGCAGAGAAATTAATAGACTTATGAAATGAATACCTGCAAGCAGATGAGGGCAA
TAAAAGACTTTTGGAACAAAGGTATGATAAGAGGGTGATTCAGAAGGCACTGGAAGAGATGGAAAGTATGGAGTGGCTAG
AGAAAAACTTCAAGAACTGCCCATGTTGTGGAACTCCCATAGAGAAATTAGATGGATATAACAAGATGACATGTACTGGC
TGTATGCAATATTTCTGTTGGATTTGCATGAGTTCTCTCTCTAGAGCAAACCGTTACAAACATTTCACTGATCCTGCTTC
ACCACGTTTTAACCAGCTGTTTTATGCTGTGGATGTTGATGAAGATATTTGGGAAGATGAGATTGAAGAC

Alignment

ORF - retro_pabe_3095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 61.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERAVQDVESLSNLIQEILDFDQAQQIKCFNSKLFLCNICFCEKLGSECMYFLECRHVYCKACLKDYFEIQ
          ...V.DVESL.N.IQEILDFDQAQQIKCFNS.LFLCNICFC.KLGSECMYFLEC.HVYCKACLKDYFEIQ
Retrocopy DSCVEDVESLLNMIQEILDFDQAQQIKCFNSNLFLCNICFCKKLGSECMYFLECTHVYCKACLKDYFEIQ

Parental  IRDGQVQCLNCPEPKCPSVATPGQVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQLPVMQEPGC
          IRDGQVQCLNCPEPKCPSVATPGQVKELVEAELFA.YD.LLLQS.LDLMADVVYCP.PCCQLPVMQEPGC
Retrocopy IRDGQVQCLNCPEPKCPSVATPGQVKELVEAELFAHYDCLLLQSTLDLMADVVYCPHPCCQLPVMQEPGC

Parental  TMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGKRVIQKALEEMESK
          T.GICSSCNFAFCTLCRLTYHGVSPCKVTAEKL.DL.NEYLQADE.NKRLL.QRY.KRVIQKALEEMES.
Retrocopy TVGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLIDL*NEYLQADEGNKRLLEQRYDKRVIQKALEEMESM

Parental  EWLEKNSKSCPCCGTPIEKLDGCNKMTCTGCMQYFCWICMGSLSRANPYKHFNDPGSPCFNRLFYAVDVD
          EWLEKN.K.CPCCGTPIEKLDG.NKMTCTGCMQYFCWICM.SLSRAN.YKHF.DP.SP.FN.LFYAVDVD
Retrocopy EWLEKNFKNCPCCGTPIEKLDGYNKMTCTGCMQYFCWICMSSLSRANRYKHFTDPASPRFNQLFYAVDVD

Parental  DDIWEDEVED
          .DIWEDE.ED
Retrocopy EDIWEDEIED

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	0.17 RPM	46.00 RPM
SRP007412_cerebellum	0.12 RPM	43.78 RPM
SRP007412_heart	0.03 RPM	35.64 RPM
SRP007412_kidney	0.03 RPM	41.20 RPM
SRP007412_liver	0.09 RPM	29.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3095 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3095 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3790
Pan troglodytes	retro_ptro_2571
Macaca mulatta	retro_mmul_1647

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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,