RetrogeneDB ID: retro_ptro_1816

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:118614946..118615679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSPTRG00000013043
• Aliases: None
• Description: None

Sequence

>retro_ptro_1816
ATGAACAACAAATTTGATGCTTTGAAAGATGACAACAATAGGGACCATGATCAGAATGAAGAAAGCAGCACACAGAAAGA
TACTGAGAAAGAAAAAACACAATGGGACAAGAATAAGAGCAGTAACAAGAGGAAGGCTGTTGTCCCTGGACAGGCAGAAC
ATCCCCTGCAGTACAACTACACTTTCTGGTACTCCAGGAGAACCCCTGGCTGTCCCACCAGCTCACAGAGTTATGAACAG
AATATCAAACAGATTGGCACCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTTATAGCCACATGGTATGTCCAAAGGATCT
GACAGGCCACAGTGACTTCGATCTCTTCAAAAAGGAATTAAACCCACGTGGGAGGATAATGCAAATAAAAATGGTGACAA
GAGGATTATTTGGCTGCGGAAGGGCTTGATCCCCCATTGCTGGGAGAATCTCATTTTGGCCATGTTGGGGGAAAAGTTCA
TGGTTGGGGAGGAGATCTGTGGGGCTGTGGTCTCTCTTCACTGTCAAGAGGACATTATTTCAATATGGAAAAGACTGCCA
GTGACCAAGCAACCACAACGTGAATCCGGGATACACTTTGGCGAGTGCTTAACCTATCTCCCAACACCATTATGAAATAC
AAAACTCACACCGACAGCATCAAAACGCCATGCAGCCTGGGCTCCCAAAGGCTCCTTTATCACAACCTCTGGAAGCTGCG
GTTGAATGTGCCA

Alignment

ORF - retro_ptro_1816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTERDKNQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPG
          MNNKFDALKDD...DHDQNEE.STQKD.EKEKT..DKN.SS.KRKAVVPG.AEHPLQYNYTFWYSRRTPG
Retrocopy MNNKFDALKDDNNRDHDQNEESSTQKDTEKEKTQWDKNKSSNKRKAVVPGQAEHPLQYNYTFWYSRRTPG

Parental  RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFK-EGIKPMWEDDANKNGGKWIIRL
          .PTSSQSYEQNIKQIGTFASVEQFWRFYSHMV.P.DLTGHSDF.LFK..GIKP.WED.ANKNG.K.II.L
Retrocopy CPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVCPKDLTGHSDFDLFK<KGIKPTWEDNANKNGDKRIIWL

Parental  RKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIW-NKTASDQATTARIRDTLRRVLNLPP
          RKGL...CWENLILAMLGE.FMVGEEICGAVVS...QEDIISIW..KTASDQATT..IRDTL.RVLNL.P
Retrocopy RKGLIPHCWENLILAMLGEKFMVGEEICGAVVSLHCQEDIISIW<EKTASDQATTT*IRDTLWRVLNLSP

Parental  NTIMEYKTHTDSIKMPGRLGPQRLLFQNLWKPRLNVP
          NTIM.YKTHTDSIK.P..LG.QRLL..NLWK.RLNVP
Retrocopy NTIMKYKTHTDSIKTPCSLGSQRLLYHNLWKLRLNVP

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	0.05 RPM	10.49 RPM
SRP007412_cerebellum	0.00 RPM	22.55 RPM
SRP007412_heart	0.00 RPM	19.00 RPM
SRP007412_kidney	0.34 RPM	22.91 RPM
SRP007412_liver	0.00 RPM	39.84 RPM
SRP007412_testis	0.00 RPM	52.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1816 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1816 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2689

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Equus caballus	ENSECAG00000020187	2 retrocopies	retro_ecab_300, retro_ecab_847,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57, retro_eeur_668,
Homo sapiens	ENSG00000135930	1 retrocopy	retro_hsap_2689,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Nomascus leucogenys	ENSNLEG00000014333	1 retrocopy	retro_nleu_1189,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816 ,
Pan troglodytes	ENSPTRG00000016301	4 retrocopies	retro_ptro_1159, retro_ptro_1386, retro_ptro_1957, retro_ptro_2672,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
Tupaia belangeri	ENSTBEG00000004455	11 retrocopies	retro_tbel_1299, retro_tbel_2197, retro_tbel_2623, retro_tbel_2680, retro_tbel_3932, retro_tbel_4471, retro_tbel_4622, retro_tbel_536, retro_tbel_616, retro_tbel_650, retro_tbel_714,