RetrogeneDB ID: retro_pabe_1788

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:32984840..32985722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPF2
• Ensembl ID: ENSPPYG00000016925
• Aliases: None
• Description: ribosome production factor 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20870]

Sequence

>retro_pabe_1788
ATAGATGCTCTGGATCGAGTTGTAAATCCCAAAATGAAAAGAGTCAAGAGATTCCTTGAGAAGAGAGAACCAAAACTCAA
TGAAATATTAAAAATGCCATGCTGATTAAAGGGGGAAATGCAAATGCAACAGTGACACAAGTACTTAAAGATGTGTGTGC
ACTGAAAAAACCATACGGTGTACTGTATAAAAAGAAAAATATTACAAGACCTTTTGAGGATCAGACATCACTGGAATTAT
TTTCAAAGAAATCAGATTGTTCTTTATTCATGTTTGGCTCCTATAATAAGAAGCGGCCAAATAATCTAGTAATAGGTCAT
ATGTATGACTACCATGTGCTGGATATGATTGAATTAGGTATTGAGAATTTTGTCTTTCTAAAAGACATTAAGAAGAGTAA
ATGTCCTGAGGGAACAAAACCCAGGCTAATATTTGCTGGTGATGATTTCAATGTAACAGAAGATTACAGAAGACTAAAAA
GTCTTCTTCTTGATTTCTTCAGAGGCCCCACGGTATCAAATATCTGCCTGGCTGGATTAGAATATGTTCTGCACTTCACT
GCACTGAATGGGAAGATTTACTTTTGAAGCTATAAGTTGCTGTTGAAGAAATCTGGTTGCGGAACACCACGGATTGAATT
GGAAGAGATAGGACTCTCCTTGAATCTGGTTCTGAGGAGGACACACCTGGCATCCGATGACCTTTATAAATTATCTATGA
AAATGCCAAAAGCTCTCAAGCCAAAGAAGAAGAAAAATATCTCCAATGATACTTTTTGTACAACTTATGGAAGGATTCAT
ATGTAGAACCAAGACAAGCAAACTACAAACCAGGAAAATGAAGGGGTTGAAGAAGCGACCTGCAGAAAGGATAACAGAAG
AC

Alignment

ORF - retro_pabe_1788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.21 %
• Parental protein coverage: 96.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDTLDRVVKPKTKRAKRFLEKREPKLNE-NIKNAMLIKGGNANATVTQVLKDVYALKKPYGVLYKKKNIT
          .D.LDRVV.PK.KR.KRFLEKREPKLNE.NIKNAMLIKGGNANATVTQVLKDV.ALKKPYGVLYKKKNIT
Retrocopy IDALDRVVNPKMKRVKRFLEKREPKLNE<NIKNAMLIKGGNANATVTQVLKDVCALKKPYGVLYKKKNIT

Parental  RPFEDQTSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGT
          RPFEDQTSLE.FSKKSDCSLFMFGS.NKKRPNNLVIG.MYDYHVLDMIELGIENFV.LKDIK.SKCPEGT
Retrocopy RPFEDQTSLELFSKKSDCSLFMFGSYNKKRPNNLVIGHMYDYHVLDMIELGIENFVFLKDIKKSKCPEGT

Parental  KPMLIFAGDDFDVTEDYRRLKSLLIDFFRGPTVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKSGCRT
          KP.LIFAGDDF.VTEDYRRLKSLL.DFFRGPTVSNI.LAGLEYVLHFTALNGKIYF.SYKLLLKKSGC.T
Retrocopy KPRLIFAGDDFNVTEDYRRLKSLLLDFFRGPTVSNICLAGLEYVLHFTALNGKIYF*SYKLLLKKSGCGT

Parental  PRIELEEMGPSLDLVLRRTHLASDDLYKLSMKMPKALKPKKKKNISHDTFGTTYGRIHMQKQDLSKLQTR
          PRIELEE.G.SL.LVLRRTHLASDDLYKLSMKMPKALKPKKKKNIS.DTF.TTYGRIHM..QD.......
Retrocopy PRIELEEIGLSLNLVLRRTHLASDDLYKLSMKMPKALKPKKKKNISNDTFCTTYGRIHM*NQD-KQTTNQ

Parental  KMKGLK-KRPAERITED
          ...G...KRPAERITED
Retrocopy ENEGVE>KRPAERITED

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	15.92 RPM
SRP007412_cerebellum	0.00 RPM	20.92 RPM
SRP007412_heart	0.00 RPM	9.63 RPM
SRP007412_kidney	0.00 RPM	11.83 RPM
SRP007412_liver	0.00 RPM	14.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1788 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1788 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2425
Pan troglodytes	retro_ptro_1398
Gorilla gorilla	retro_ggor_83

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003918	2 retrocopies	retro_cfam_1611, retro_cfam_903,
Callithrix jacchus	ENSCJAG00000005212	6 retrocopies	retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus	ENSCPOG00000006797	2 retrocopies	retro_cpor_332, retro_cpor_582,
Equus caballus	ENSECAG00000017121	1 retrocopy	retro_ecab_782,
Erinaceus europaeus	ENSEEUG00000006169	2 retrocopies	retro_eeur_454, retro_eeur_584,
Felis catus	ENSFCAG00000001527	1 retrocopy	retro_fcat_1584,
Homo sapiens	ENSG00000197498	1 retrocopy	retro_hsap_2425,
Gorilla gorilla	ENSGGOG00000001469	1 retrocopy	retro_ggor_83,
Myotis lucifugus	ENSMLUG00000005676	2 retrocopies	retro_mluc_485, retro_mluc_921,
Macaca mulatta	ENSMMUG00000021532	1 retrocopy	retro_mmul_1903,
Mus musculus	ENSMUSG00000038510	1 retrocopy	retro_mmus_2234,
Nomascus leucogenys	ENSNLEG00000012854	3 retrocopies	retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus	ENSOCUG00000016028	1 retrocopy	retro_ocun_831,
Pongo abelii	ENSPPYG00000016925	2 retrocopies	retro_pabe_1788 , retro_pabe_2464,
Pan troglodytes	ENSPTRG00000018503	1 retrocopy	retro_ptro_1398,
Rattus norvegicus	ENSRNOG00000000587	1 retrocopy	retro_rnor_2336,
Tupaia belangeri	ENSTBEG00000017151	9 retrocopies	retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,