RetrogeneDB ID: retro_hsap_2106

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:58478565..58479657(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233426
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSG00000175390
• Aliases: EIF3F, EIF3S5, eIF3-p47
• Description: eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]

Sequence

>retro_hsap_2106
CTCGACAAGATGGCCACACCGGCGGTACCAGCAAGTGCTCCTCCGGCCACGCCAGCCCCAGTCCCGGCGGCGGTCCCAGC
CTCTGCCCCAGCCTCAGTTCCAGCGCCAACGCCAGCACCGGCTGCGGCTCCGGTTCCCGCTGCGGCTCCAGCCTCATCCT
CAGACCCTGCGGCAGCATCGGCTACAACTGCGGCTCCTGGCCAGACCCCGGCCTCAGCGCAAGCTCCAGCGCAGACCCCA
GCGCCCGCTCTGCCTGGTCCTGCTCTTCCAGGGCCCTTCCCCGGCGGCCGCGTGGTCAGGCTGCACCCAGTCATTTTGGC
CTCCATTGTGGACAGCTACGAGAGACGCAACGAGGGTGCTGCCCGAGTTATCGGGACCCTGTTGGGAACTGTCGACAAAC
ACTCAGTGGAGGTCACCAATTGCTTTTCAGTGCCGCACAATGAGTCAGAAGATGAAGTGGCTGTTGACATGGAATTTGCT
AAGAATATGTATGAACTGCATAAAAAAGTTTCTCCAAATGAGCTCATCCTGGGCTGGTACGCTACAGGCCATGACATCAC
AGAGCACTCTGTGCTGATCCATGAGTACTACAGCCGAGAGGCCCCCAACCCCATCCACCTCACTGTGGACACAAGTCTCC
AGAACGGCCGCATGAGCATCAAAGCCTATGTCAGCACTTTAATGGGTGTCCCTGGGAGGACCATGGGAGTGATGTTCACA
CCTCTGACAGTGAAATACGCATACTATGACACTGAACGCATCGGAGTTGAGCTGATCATGAAGACCTGCTTTAGCCCCAA
CAGAGTGATTGGACTCTTAAGTGACTTGCAGCAAGTAGGAGGGGCATCAGCTCGCATCCAGGATGCCCTGAGTACAGTGT
TGCAATATGCAGAGGATGTACTGTCTGGAAAGGTGTCAGCTGACAATACTGTGGGCCGCTTCCTGATGAGCCTGGTTAAC
CGAGTACCGAAAATAGTTCCCGATGACTTTGAGACCATGCTCAACAGCAACATCAATGACCTTTTGATGGTGACCTACCT
GGCCAACCTCACACAGTCACAGATTGCCCTCAATGAAAAACTTGTAAACCTG

Alignment

ORF - retro_hsap_2106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.7 %
• Parental protein coverage: 96.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKMATPAVPVSAPPATPTP----VPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPGQTP
          LDKMATPAVP.SAPPATP.P....VPA.APASVPAPTPAPAAAPVPAAAPASSSDPAAA.A.TAAPGQTP
Retrocopy LDKMATPAVPASAPPATPAPVPAAVPASAPASVPAPTPAPAAAPVPAAAPASSSDPAAASATTAAPGQTP

Parental  ASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTN
          ASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTN
Retrocopy ASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTN

Parental  CFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVD
          CFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVD
Retrocopy CFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVD

Parental  TSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVG
          TSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGV.LIMKTCFSPNRVIGL.SDLQQVG
Retrocopy TSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVELIMKTCFSPNRVIGLLSDLQQVG

Parental  GASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANL
          GASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVN.VPKIVPDDFETMLNSNINDLLMVTYLANL
Retrocopy GASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNRVPKIVPDDFETMLNSNINDLLMVTYLANL

Parental  TQSQIALNEKLVNL
          TQSQIALNEKLVNL
Retrocopy TQSQIALNEKLVNL

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
bodymap2_adipose	5.05 RPM	123.58 RPM
bodymap2_adrenal	0.61 RPM	167.34 RPM
bodymap2_brain	2.27 RPM	61.18 RPM
bodymap2_breast	1.28 RPM	98.97 RPM
bodymap2_colon	5.63 RPM	168.38 RPM
bodymap2_heart	0.15 RPM	74.14 RPM
bodymap2_kidney	2.01 RPM	83.03 RPM
bodymap2_liver	0.63 RPM	43.79 RPM
bodymap2_lung	1.05 RPM	104.24 RPM
bodymap2_lymph_node	2.03 RPM	130.82 RPM
bodymap2_ovary	2.83 RPM	198.17 RPM
bodymap2_prostate	3.48 RPM	207.30 RPM
bodymap2_skeletal_muscle	1.93 RPM	135.19 RPM
bodymap2_testis	3.47 RPM	138.80 RPM
bodymap2_thyroid	0.96 RPM	107.73 RPM
bodymap2_white_blood_cells	2.38 RPM	225.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2106 was not detected

EST

No EST(s) were mapped for retro_hsap_2106 retrocopy.

TSS

No TSS is located nearby retro_hsap_2106 retrocopy 5' end.

Lab

retro_hsap_2106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2106 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Homo sapiens	ENSG00000175390	3 retrocopies	retro_hsap_2106 , retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,