RetrogeneDB ID: retro_pabe_2279

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:946632..947194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSPPYG00000016409
• Aliases: None
• Description: proline rich 3 [Source:HGNC Symbol;Acc:21149]

Sequence

>retro_pabe_2279
ATGCCGAAATGGAAGAAGCAGAATCAGCACCAGCCCCCGCCACAGCAGCAGCCCCTACCGCCCGAGAGGGAAAAGACTGG
AGATGACGAGGATGGGAGTCCCATCGGATCACCCAGCCTTCTTGAGCCACCCCCCATGGCCAGTGGAAAACCTGATGACC
CTAAGTCAGCTCCTCACAGAGGTCCTCCAAGAGCAAGGGGACCGCTGATTCCACCGCTCCTGAGCCTCCCACCTCCTCCT
CAGGGTAGAGGCCCAATGCCAGGAGGCCTTGGCCCCAGGCCTAGCCCATATGATTGTGGTTGGTGGGCAGTCAATGCCGA
ACCTCCTTTTCCGGGGCCAGGCCATGGGGGTCCCGCCAGGCAAAGCCTTCACAAAGAACAGAGAAACCCTCAAAGGCTCG
AAAGCTGGTCTCTTATCAAGAATACCAGCCTACTAGGATGACCCCCAGGTTATGGAAGACAAATCCCACCGCCCAGTCTG
TGGACATTTTGCCAAAAAGGGCCACTGTTGATACGATGACCTCTGTACCTTCCACCACCCAGGCATCAATAGCCCTCCTC
TG

Alignment

ORF - retro_pabe_2279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKRKKQNQHQPPTQQQPPLPEREETGDEEDGSPIGPPSLLGPPPMANGKPGDPKSALHRGPPGSRGPLI
          MPK.KKQNQHQPP.QQQP..PERE.TGD.EDGSPIG.PSLL.PPPMA.GKP.DPKSA.HRGPP..RGPLI
Retrocopy MPKWKKQNQHQPPPQQQPLPPEREKTGDDEDGSPIGSPSLLEPPPMASGKPDDPKSAPHRGPPRARGPLI

Parental  PPLLSLPPPPWGRGPIWRGLGPRSSPYGRGWWGVNAEPPFPGPGHGGPTRGSFHKEQRNPRRLKSWSLIK
          PPLLSLPPPP.GRGP...GLGPR.SPY..GWW.VNAEPPFPGPGHGGP.R.S.HKEQRNP.RL.SWSLIK
Retrocopy PPLLSLPPPPQGRGPMPGGLGPRPSPYDCGWWAVNAEPPFPGPGHGGPARQSLHKEQRNPQRLESWSLIK

Parental  NTC-PPKDDP-QVMEDKSDRPVCRHFAKKGHCRYEDLCAFYHPGVNGPPL
          NT..P....P.QVMEDKS.RPVC.HFAKKGHC.Y.DLC.F.HPG.N.PPL
Retrocopy NTS<PTRMTP<QVMEDKSHRPVCGHFAKKGHC*YDDLCTFHHPGINSPPL

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	0.06 RPM	15.98 RPM
SRP007412_cerebellum	0.00 RPM	18.00 RPM
SRP007412_heart	0.00 RPM	1.72 RPM
SRP007412_kidney	0.00 RPM	7.46 RPM
SRP007412_liver	0.00 RPM	3.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2279 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2279 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1861
Gorilla gorilla	retro_ggor_1915

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279 ,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,