RetrogeneDB ID: retro_ptro_1594

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:43357389..43357613(-)
• Located in intron of: ENSPTRG00000011867

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYCBP
• Ensembl ID: ENSPTRG00000000565
• Aliases: None
• Description: MYC binding protein [Source:HGNC Symbol;Acc:7554]

Sequence

>retro_ptro_1594
CACTATGGCCCATTAGAACACTGCTAACTCCAAGATCAAGCAATTCTGGAGGTGCTTAGGGCTCTGGGGTGCTGAACGAA
GGTGCTGGTAGCCTTAGAAAAGAACCAGAGAAACCTAATACTGCTTAGGTTTTTTTAAAGCATCACTTAGGAGTTGCTAT
CCCAGAAAATCCAGAAATAGAACTGCTTCCCCTAGAATTGACAGAAATGAAAGATAAATATGAA

Alignment

ORF - retro_ptro_1594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 72.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HYKAADSKREQFRRYLEKSGVLDTLTKVLVALYE-EPEKPNSALDFLKHHLGAATPENPEIELLRLELAE
          HY........Q....LE....L...TKVLVAL...EPEKPN.A..FLKHHLG.A.PENPEIELL.LEL.E
Retrocopy HYGPLEHC*LQDQAILEVLRALGC*TKVLVALEK<EPEKPNTA*VFLKHHLGVAIPENPEIELLPLELTE

Parental  MKEKYE
          MK.KYE
Retrocopy MKDKYE

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	0.04 RPM	3.81 RPM
SRP007412_cerebellum	0.00 RPM	6.31 RPM
SRP007412_heart	0.00 RPM	6.70 RPM
SRP007412_kidney	0.00 RPM	22.33 RPM
SRP007412_liver	0.00 RPM	7.07 RPM
SRP007412_testis	0.00 RPM	29.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1594 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1594 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1678

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030622	1 retrocopy	retro_cfam_1618,
Choloepus hoffmanni	ENSCHOG00000013136	3 retrocopies	retro_chof_1349, retro_chof_151, retro_chof_610,
Callithrix jacchus	ENSCJAG00000036558	1 retrocopy	retro_cjac_5,
Cavia porcellus	ENSCPOG00000020447	1 retrocopy	retro_cpor_1195,
Homo sapiens	ENSG00000214114	2 retrocopies	retro_hsap_1649, retro_hsap_2251,
Gorilla gorilla	ENSGGOG00000005810	2 retrocopies	retro_ggor_1245, retro_ggor_1678,
Loxodonta africana	ENSLAFG00000020514	2 retrocopies	retro_lafr_1071, retro_lafr_903,
Macropus eugenii	ENSMEUG00000000315	1 retrocopy	retro_meug_247,
Mus musculus	ENSMUSG00000028647	1 retrocopy	retro_mmus_1626,
Nomascus leucogenys	ENSNLEG00000011814	2 retrocopies	retro_nleu_1319, retro_nleu_2489,
Oryctolagus cuniculus	ENSOCUG00000022203	2 retrocopies	retro_ocun_907, retro_ocun_979,
Otolemur garnettii	ENSOGAG00000024435	3 retrocopies	retro_ogar_1283, retro_ogar_1553, retro_ogar_1880,
Pongo abelii	ENSPPYG00000001515	1 retrocopy	retro_pabe_1400,
Pan troglodytes	ENSPTRG00000000565	2 retrocopies	retro_ptro_1120, retro_ptro_1594 ,
Rattus norvegicus	ENSRNOG00000017166	2 retrocopies	retro_rnor_573, retro_rnor_779,
Sus scrofa	ENSSSCG00000003649	2 retrocopies	retro_sscr_1176, retro_sscr_1217,
Ictidomys tridecemlineatus	ENSSTOG00000021547	2 retrocopies	retro_itri_1518, retro_itri_252,
Tarsius syrichta	ENSTSYG00000005690	1 retrocopy	retro_tsyr_172,
Tursiops truncatus	ENSTTRG00000009583	1 retrocopy	retro_ttru_1872,