RetrogeneDB ID: retro_hsap_2512

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:11180922..11181815(-)
• Located in intron of: ENSG00000271308

Retrocopy information

• Ensembl ID: ENSG00000234643
• 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_2512
CAGACCCTGGCCTCAGCACAAGCTCCAGCGCAGACCCCAGCAACCGCTCTGCCTGGTCCTGTTCTTCCAGGGCCCTTCCC
TGGTGGCCGTGTGGTCAGGCTGCACCCAGTCATTTTGGCCTCCACTGTGGACAGCTACGAGAGACGCAACAAGGGTGCTG
CCCGAGTTATCGGGACCCTGTTGGGAACTGTCAACAAACACTCAGTGGAGGTCACCAGTTGCTTTTCAGTGTCACACAAT
GAGTCAGATGAAGTGGCTGTTGACATGGAATTTGCTAAGAACATGTATGAACTGCCTAAAAAGTTTCTCCAAATGAGCTC
ATCTTGGGGTGGTACGCTGCAGGCCATGACATCACAGAGCACTCTGTGCTGATCCATGAGTACTACAGCCGAGAGGCCCC
CAACCCCATCCACCTCACTGTGGACACAAGTCTCCAGAACGGCCATATGAGCATCAAAGCCTATGTCAGCACTTTAATGG
GTGTCCCTGGGAGGATCGTGGGAGTGTTCACACCTCTGACAGTGAAATACGCATTCTATGACACTGAATGCATCAGAGTT
GACCTGATCATGAAGACCTGCTTTAGCCCCAACAGAGTGGTTGGACTCTCAAGTGACTTGCAGCAAGTAGGAGGGGCATC
AGCTCGCATCCAGGATACCCTGAGCATAGTGTTGCAATATGCAGAGGATATACTATCTGGAAAGGTGTCAGCTGACAATA
CCATCAGGAAGGTGGGCCACTTCCTGATGAGCCTGGTTAACCAAGTACCAAAAATAGTTCCCGATGACTTCGAGACCATG
CTCCACAGCAACATCAATGACCTGTTGATGGTGACCTAACTGGCCAACCTCACACAGTCACAGATTGCCCTCAATGAAAA
ACTTGTAAACCTG

Alignment

ORF - retro_hsap_2512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 83.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVE
          QT.ASAQAPAQTPA.ALPGP.LPGPFPGGRVVRLHPVILAS.VDSYERRN.GAARVIGTLLGTV.KHSVE
Retrocopy QTLASAQAPAQTPATALPGPVLPGPFPGGRVVRLHPVILASTVDSYERRNKGAARVIGTLLGTVNKHSVE

Parental  VTNCFSVPHNESEDEVAVDMEFAKNMYELHK-KVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIH
          VT.CFSV.HNES.DEVAVDMEFAKNMYEL.K.KVSPNELILGWYA.GHDITEHSVLIHEYYSREAPNPIH
Retrocopy VTSCFSVSHNES-DEVAVDMEFAKNMYELPK<KVSPNELILGWYAAGHDITEHSVLIHEYYSREAPNPIH

Parental  LTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDL
          LTVDTSLQNG.MSIKAYVSTLMGVPGR..GV.FTPLTVKYA.YDTE.I.VDLIMKTCFSPNRV.GLSSDL
Retrocopy LTVDTSLQNGHMSIKAYVSTLMGVPGRIVGV-FTPLTVKYAFYDTECIRVDLIMKTCFSPNRVVGLSSDL

Parental  QQVGGASARIQDALSTVLQYAEDVLSGKVSADNT---VGRFLMSLVNQVPKIVPDDFETMLNSNINDLLM
          QQVGGASARIQD.LS.VLQYAED.LSGKVSADNT...VG.FLMSLVNQVPKIVPDDFETML.SNINDLLM
Retrocopy QQVGGASARIQDTLSIVLQYAEDILSGKVSADNTIRKVGHFLMSLVNQVPKIVPDDFETMLHSNINDLLM

Parental  VTYLANLTQSQIALNEKLVNL
          VT.LANLTQSQIALNEKLVNL
Retrocopy VT*LANLTQSQIALNEKLVNL

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	0.06 RPM	123.58 RPM
bodymap2_adrenal	0.00 RPM	167.34 RPM
bodymap2_brain	0.00 RPM	61.18 RPM
bodymap2_breast	0.00 RPM	98.97 RPM
bodymap2_colon	0.00 RPM	168.38 RPM
bodymap2_heart	0.00 RPM	74.14 RPM
bodymap2_kidney	0.00 RPM	83.03 RPM
bodymap2_liver	0.02 RPM	43.79 RPM
bodymap2_lung	0.00 RPM	104.24 RPM
bodymap2_lymph_node	0.00 RPM	130.82 RPM
bodymap2_ovary	0.00 RPM	198.17 RPM
bodymap2_prostate	0.00 RPM	207.30 RPM
bodymap2_skeletal_muscle	0.00 RPM	135.19 RPM
bodymap2_testis	0.02 RPM	138.80 RPM
bodymap2_thyroid	0.00 RPM	107.73 RPM
bodymap2_white_blood_cells	0.00 RPM	225.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2512 was not detected

EST

No EST(s) were mapped for retro_hsap_2512 retrocopy.

TSS

No TSS is located nearby retro_hsap_2512 retrocopy 5' end.

Lab

retro_hsap_2512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2512 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,