RetrogeneDB ID: retro_pabe_80

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:122253825..122254611(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020693
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MRRF
• Ensembl ID: ENSPPYG00000019570
• Aliases: None
• Description: mitochondrial ribosome recycling factor [Source:HGNC Symbol;Acc:7234]

Sequence

>retro_pabe_80
ATGGCCTTGGGATTAAAGTGCTCCCGCATGGTCCACCCTGCCTTTCGCAATTATCTTGCAGCCTCTATCAGACCCGTTTT
AGAAGTTACACTGAAGACAGTGCATGAAAGACAACACGGCCGTAGGCAATACATGGCCTATTCAGCTGTACCAGTCCACC
ATTTTGCTACCAAGAAAGCCAAAGCCAAAGGGAAAGGAAAGTCCCAAACCAGAGTGAATATTAGTGCTGCCTTTGTTGAG
GATATAATCAACTTGGAAGAGGTGAATGAAGAAATGAAGTCTGTGATAGAAGCACTCAAGGATAATTTCAATAAGACTCT
CAATATAAGGACCTCACCAGGATCCCTTGACAAGATTGCTGTGGTAACTGCTGATGGGAAACTTGCTTTAAACCAGATTA
GCCAGATCTCCATGAAGTCGCCACAGCTGATTTTGGTGAATATGGCCAGCTTCCCAGAGTGTACAGCTGCAGCTATCAAG
GCTATAAGAGAAAGTGGAATGAATCTGAATCCAGAAGTGGAAGGGGCACTAATTCGGGTACCCATTCCCCAAGTAATCAG
AGAGCACAGAGAAATGCTGGTGAAACTGGCCAAACAGAACACCAACAAGGCCAAATACTCTTTATGGAAGGTTTGTACCA
ATGCAATGAACAAGCTGAAGAAATCCAAGGATACAGTCTCGGAGGATACCATTAGGCTAACAGAGAAACAGATCAGCCAA
ATGGCCGATGACACAGTGGCAGAATTGGACAGGCATCTGGCAGTGAAGACCAAAGAACTCCTTGGA

Alignment

ORF - retro_pabe_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALGLKCFRMVHPAFRNYLAASIRPVSEVTLKTVHERQHGHRQYMDYSAVPVRHFATKKAKAKGKGQSQT
          MALGLKC.RMVHPAFRNYLAASIRPV.EVTLKTVHERQHG.RQYM.YSAVPV.HFATKKAKAKGKG.SQT
Retrocopy MALGLKCSRMVHPAFRNYLAASIRPVLEVTLKTVHERQHGRRQYMAYSAVPVHHFATKKAKAKGKGKSQT

Parental  RVNINAALVEDIINLEEVNEEMKSVIEALKDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQISQISMKS
          RVNI.AA.VEDIINLEEVNEEMKSVIEALKDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQISQISMKS
Retrocopy RVNISAAFVEDIINLEEVNEEMKSVIEALKDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQISQISMKS

Parental  PQLILVNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPIPQVTREHREMLVKLAKQNTNKAKDSLRK
          PQLILVNMASFPECTAAAIKAIRESGMNLNPEVEG.LIRVPIPQV.REHREMLVKLAKQNTNKAK.SL.K
Retrocopy PQLILVNMASFPECTAAAIKAIRESGMNLNPEVEGALIRVPIPQVIREHREMLVKLAKQNTNKAKYSLWK

Parental  VRTNSMNKLKKSKDTVSEDTIRLIEKQISQMADDTVAELDRHLAVKTKELLG
          V.TN.MNKLKKSKDTVSEDTIRL.EKQISQMADDTVAELDRHLAVKTKELLG
Retrocopy VCTNAMNKLKKSKDTVSEDTIRLTEKQISQMADDTVAELDRHLAVKTKELLG

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	9.23 RPM
SRP007412_cerebellum	0.00 RPM	11.67 RPM
SRP007412_heart	0.00 RPM	10.45 RPM
SRP007412_kidney	0.13 RPM	14.75 RPM
SRP007412_liver	0.00 RPM	10.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_80 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_80 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_80 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4897
Pan troglodytes	retro_ptro_3265
Gorilla gorilla	retro_ggor_98

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80 ,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411,