RetrogeneDB ID: retro_ptro_197

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:128755514..128756090(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSPTRG00000003326
• Aliases: EIF3F, EIF3S5
• Description: Pan troglodytes eukaryotic translation initiation factor 3, subunit F (EIF3F), mRNA. [Source:RefSeq mRNA;Acc:NM_001110812]

Sequence

>retro_ptro_197
AATGAGCTCATCCTGGGCTGGTAGGCTACAGGCCATGACATCACAGAACACTCTGTGCTGATTCATAAGTACTACAGCCT
GATGGCCCCCAACCCCATCCGCCTCACTGTGGTCAGAAGTCTCCAGAACCACTGCATGAGCATCAAACCCTATGTCAGTA
CTTTAATGGGTGTCCCTGGGAGGACCATGGGAGTGATGTTCACACCTCTGACAGTGATGTATGCATACTATGACACTGAA
TGCCTTGGAGTTGACCTGATTATGAAGACCTGTTTTAACCCCAGCTAAGGGATCCGACTCTCAAGTGACTTGCAGCAAGT
AGGAGGGGCATCAGCTTGCATCCAGGATGTCCTAGGCACAGTGTTGCAATATGCAGAGGATGTACTGTCTGGAAAGATGT
CAGCTGACAATACTGTGGACCACTTCTTAACAAGCCTGGTTAAGCAAGTATCCAAAATAGTTACCAGTGATTTCGAGAGC
ATGCTCAACAGCAACATCAAGGACCTGCTGATGGTGACCTACCTGGCCAATCTCACACAGTCATAGATTGCCCTCAATGA
GAAACTTGTAAACCTG

Alignment

ORF - retro_ptro_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 53.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPL
          NELILGW.ATGHDITEHSVLIH.YYS..APNPI.LTV..SLQN..MSIK.YVSTLMGVPGRTMGVMFTPL
Retrocopy NELILGW*ATGHDITEHSVLIHKYYSLMAPNPIRLTVVRSLQNHCMSIKPYVSTLMGVPGRTMGVMFTPL

Parental  TVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSADNTVG
          TV.YAYYDTE..GVDLIMKTCF.P...I.LSSDLQQVGGASA.IQD.L.TVLQYAEDVLSGK.SADNTV.
Retrocopy TVMYAYYDTECLGVDLIMKTCFNPS*GIRLSSDLQQVGGASACIQDVLGTVLQYAEDVLSGKMSADNTVD

Parental  RFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
          .FL.SLV.QV.KIV..DFE.MLNSNI.DLLMVTYLANLTQS.IALNEKLVNL
Retrocopy HFLTSLVKQVSKIVTSDFESMLNSNIKDLLMVTYLANLTQS*IALNEKLVNL

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	1.04 RPM	63.31 RPM
SRP007412_cerebellum	1.43 RPM	63.74 RPM
SRP007412_heart	0.20 RPM	52.29 RPM
SRP007412_kidney	0.60 RPM	134.68 RPM
SRP007412_liver	0.13 RPM	65.86 RPM
SRP007412_testis	3.48 RPM	68.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_197 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_197 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_412

---

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	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 ,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,