RetrogeneDB ID: retro_pabe_1400

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:59501981..59502188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYCBP
• Ensembl ID: ENSPPYG00000001515
• Aliases: MYCBP, AMY1
• Description: C-Myc-binding protein [Source:UniProtKB/Swiss-Prot;Acc:Q5R7A8]

Sequence

>retro_pabe_1400
TATGAAGAACCAGAGAAACCTAACGGTGCTTTGGATTTCTTAAAGCATCACTTAGGAACTGCTACCCCAGAAAATCCAGA
AATAGAGCTGCTTTGCCTAGAACTGGCAAAAACGAAAGAGAAATATAAAGCTATTGTAGAAAAAAGTAAAAAACTGAAAG
CAAAGCTTGCTCAGTATGAACCACCTCAGGAGGAGAAGCATGCTGAA

Alignment

ORF - retro_pabe_1400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.01 %
• Parental protein coverage: 54.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YEEPEKPNSALDFLKHHLGAATPENPEIELLRLELAEIKEKYEAIVEENKKLKAKLAQYEPPQEEKRAE
          YEEPEKPN.ALDFLKHHLG.ATPENPEIELL.LEL................LKAKLAQYEPPQEEK.AE
Retrocopy YEEPEKPNGALDFLKHHLGTATPENPEIELLCLELXXXXXXXXXXXXXXXXLKAKLAQYEPPQEEKHAE

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	0.00 RPM	3.65 RPM
SRP007412_cerebellum	0.00 RPM	7.30 RPM
SRP007412_heart	0.00 RPM	8.40 RPM
SRP007412_kidney	0.00 RPM	13.19 RPM
SRP007412_liver	0.00 RPM	7.65 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1400 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1400 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1649
Pan troglodytes	retro_ptro_1120
Gorilla gorilla	retro_ggor_1245

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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,