RetrogeneDB ID: retro_cjac_2717

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:46346352..46347086(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007396
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSCJAG00000013786
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_cjac_2717
ATGAACAACAAGTTCGACGCTTTGAAAGATGATGACAGTGGGGACCATGACCAGAATGAAGAAAACAGCACACCAAAACA
TGGTGAGAAGAAAAAACAGAGCGAGATAAGAGTCAGAGCAGCAGCAAGAGAAAGGCTGTTGTCCCTGGACCGGCAGAACA
CCCCCTGCAGTACAACTACACTTTCTGGTACTCCAGGAGAACCCCCAGCCGTCCCACCAGCTCACAGAGCTATGAACAGA
ATATCAAACAGATTGGCACCTTTGCTTCTGTGGAGCATTTCTGGAGGTTTTATAGCCACATAGTACATCCTGGAGACCTG
ACAGGCCACAGTGACTTCCATCTCTTCAAGGAAGGAATTAAACCCATGTGGGAGGATGATGCAAATAAAAATGGTGGCAA
GTGGATTATTCGGCTGACGAAGGGCTTGGCCTCCTGTTGCTGGGAGAATCTCATTTTGGCCATGTTGGGGGAACAGTTCA
TGGTTGGGGAGGAGATCTGTGGGGCTGTGGTGTCTGTCAGCTTTCAGGAGGACATTATTTCAATATGGAATAAGACCGCC
AGCAACCAGGCAACCACAGCCCGAATCCGGGACACGCTTCGGCGAGTGCTTAACCTACCTCCCAACACCATTATGGAGTA
CAAAACTCACACCGACAGCATCAAAATGCCAGGCAGGCTGGGCCCCCAAAGGCTCCTTTTTCAAAACCTCTGGAAGCCAT
GGTTGAATGTGCCA

Alignment

ORF - retro_cjac_2717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTPKDGEK-EKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTP
          MNNKFDALKDDDSGDHDQNEENSTPK.GEK.EKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTP
Retrocopy MNNKFDALKDDDSGDHDQNEENSTPKHGEK<EKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTP

Parental  GRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRL
          .RPTSSQSYEQNIKQIGTFASVE.FWRFYSH.V.PGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRL
Retrocopy SRPTSSQSYEQNIKQIGTFASVEHFWRFYSHIVHPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRL

Parental  RKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPN
          .KGLAS.CWENLILAMLGEQFMVGEEICGAVVSV.FQEDIISIWNKTAS.QATTARIRDTLRRVLNLPPN
Retrocopy TKGLASCCWENLILAMLGEQFMVGEEICGAVVSVSFQEDIISIWNKTASNQATTARIRDTLRRVLNLPPN

Parental  TIMEYKTHTDSIKMPGRLGPQRLLFQNLWKPRLNVP
          TIMEYKTHTDSIKMPGRLGPQRLLFQNLWKP.LNVP
Retrocopy TIMEYKTHTDSIKMPGRLGPQRLLFQNLWKPWLNVP

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
SRP051959_colon	0.04 RPM	10.21 RPM
SRP051959_heart	0.00 RPM	6.14 RPM
SRP051959_kidney	0.00 RPM	8.54 RPM
SRP051959_liver	0.04 RPM	9.38 RPM
SRP051959_lung	0.05 RPM	8.67 RPM
SRP051959_lymph_node	0.07 RPM	10.55 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.49 RPM
SRP051959_spleen	0.02 RPM	7.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2717 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2717 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2717 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010598	2 retrocopies	retro_btau_1232, retro_btau_1498,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Choloepus hoffmanni	ENSCHOG00000013109	3 retrocopies	retro_chof_1963, retro_chof_369, retro_chof_567,
Callithrix jacchus	ENSCJAG00000007151	2 retrocopies	retro_cjac_1373, retro_cjac_2097,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717 ,
Dasypus novemcinctus	ENSDNOG00000016877	1 retrocopy	retro_dnov_1374,
Equus caballus	ENSECAG00000020187	2 retrocopies	retro_ecab_300, retro_ecab_847,
Echinops telfairi	ENSETEG00000007930	1 retrocopy	retro_etel_1385,
Homo sapiens	ENSG00000135930	1 retrocopy	retro_hsap_2689,
Macropus eugenii	ENSMEUG00000015519	2 retrocopies	retro_meug_445, retro_meug_644,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Monodelphis domestica	ENSMODG00000002680	1 retrocopy	retro_mdom_1717,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Pteropus vampyrus	ENSPVAG00000007494	4 retrocopies	retro_pvam_1147, retro_pvam_340, retro_pvam_541, retro_pvam_720,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
Ictidomys tridecemlineatus	ENSSTOG00000003508	3 retrocopies	retro_itri_1270, retro_itri_1370, retro_itri_573,
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,
Tursiops truncatus	ENSTTRG00000010927	2 retrocopies	retro_ttru_1799, retro_ttru_1920,