RetrogeneDB ID: retro_pabe_175

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:111756248..111757331(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019538
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSPPYG00000003512
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]

Sequence

>retro_pabe_175
ATGGCCACACCGGCGGTACCAGCAAGTGCTCCTGCGGCCACGCCAGCCCCAGTCCCGGCGGCGGCCCCAGCCTTGGCCCC
AGCCTCAGTTCCAGCGCCAACGCCAGCACCGGCTGCGGCTCCTACTCCCGCTGCGGCTCCAGCCTCATCCTCAAACCCTG
CGGCAGCAGCGGCTACAACTGCAGCTCCTGGCCAGACCCAGGCCTCAGCGCAAGCTCCAGCGCAGACCCCAGCGCCTGCT
CTGCCTGGTCCTGCTCTTCCAGGGCCCTTCGTCGGCGGCCGCGTGGTCAGGCTGCACCCAGTCATTTTGGCCTCCATTGT
GGACAGCTACGAGAGACGCAACGAGGGTGCTGCCCGAGTTATCGGGACCCTGTTGGGAACTGTCGACAAACACTCAGTGG
AGGTCACCAATTGCTTTTCAGTGCCGCACAATGAGTCAGAAGATGAAGTGGCTGTTGACATGGAATTTGCTAAGAATATG
TATGAACTGCATAAAAAAGTTTCTCCAAATGAGCTCATCCTGGGCTGGTACGCTACAGGCCATGACATCACAGAGCACTC
TGTGCTGATCCATGAGTACTACAGCCGAGAGGCCCCCAACCCCATCCACCTCACTGTGGACACAAGTCTCCAGAACGGCG
GCATGAGCATCAAAGCCTATGTCAGCACTTTAATGGGTGTCCCTGGGAGGACCATGGGAGTGATGTTCACACCTCTGACA
ATGAAATACGCATACTATGACACTGAACGCATCCGAGTTGACCTAATCATGAAGACCTGCTTTAGCCCCAACAGAGTGAT
TGGACTCTCAAGTGACTTGCAGCAAGTAGGAGGGGCATCAGCTCGCATCCAGGATGCCCTGAGCACAGTGTTGCAATATG
CAGAGGATGTACTGTCTGGAAAGGTGTCAGCTGACAATACTGTGGGCCGCTTCCTGATGAGCCTGGTTAACCAAGTACCA
AAAATAGTTCCTGATGACTTCCAGACCATGCTCAACAGCAACATCAATGACCTGTTGATGGTGACCTACCTGGCCAACCT
CACACAGTCACAGATTGCCCTCAATGAAAAACTTGTAAACCTG

Alignment

ORF - retro_pabe_175 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATPVVPASAPPATPAPVPAAAPASAPASVPAPTPAPAAAPVPAAAPASSSDPATAAATTAAPGQTPASA
          MATP.VPASAP.ATPAPVPAAAPA.APASVPAPTPAPAAAP.PAAAPASSS.PA.AAATTAAPGQT.ASA
Retrocopy MATPAVPASAPAATPAPVPAAAPALAPASVPAPTPAPAAAPTPAAAPASSSNPAAAAATTAAPGQTQASA

Parental  QAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTNCFS
          QAPAQTPAPALPGPALPGPF.GGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTNCFS
Retrocopy QAPAQTPAPALPGPALPGPFVGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTNCFS

Parental  VPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSL
          VPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSL
Retrocopy VPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSL

Parental  QNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGAS
          QNG.MSIKAYVSTLMGVPGRTMGVMFTPLT.KYAYYDTERI.VDLIMKTCFSPNRVIGLSSDLQQVGGAS
Retrocopy QNGGMSIKAYVSTLMGVPGRTMGVMFTPLTMKYAYYDTERIRVDLIMKTCFSPNRVIGLSSDLQQVGGAS

Parental  ARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQS
          ARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDF.TMLNSNINDLLMVTYLANLTQS
Retrocopy ARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFQTMLNSNINDLLMVTYLANLTQS

Parental  QIALNEKLVNL
          QIALNEKLVNL
Retrocopy QIALNEKLVNL

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	36.88 RPM
SRP007412_cerebellum	0.00 RPM	50.22 RPM
SRP007412_heart	0.09 RPM	39.86 RPM
SRP007412_kidney	0.17 RPM	63.91 RPM
SRP007412_liver	0.09 RPM	59.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_175 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_175 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175 ,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,