RetrogeneDB ID: retro_hsap_1649

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:72312260..72312467(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000261774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MYCBP
• Ensembl ID: ENSG00000214114
• Aliases: None
• Description: MYC binding protein [Source:HGNC Symbol;Acc:7554]

Sequence

>retro_hsap_1649
TATGAAGAACCAGAGAAACCTAACAGTGCTTTGGATTTCTTAAAGCATCACTTAGGAACTGCTACCCCAGAAAATCCAGA
AATAGAGCTGCTGTGCCTAGAACTGGCGAAAACGAAAGAGAAATATAAAGCTATTGTAGAAAAAAATAAAAAACTGAAAG
CAAAGCTTGCTCAGTATGAACCACCTCAGGAGGAGAAGTATGCTGAA

Alignment

ORF - retro_hsap_1649 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 66.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YEEPEKPNSALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLKAKLAQYEPPQEEKRAE
          YEEPEKPNSALDFLKHHLG.ATPENPEIELL.LELA..KEKY.AIV.....LKAKLAQYEPPQEEK.AE
Retrocopy YEEPEKPNSALDFLKHHLGTATPENPEIELLCLELAKTKEKYKAIVXXXXXLKAKLAQYEPPQEEKYAE

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
bodymap2_adipose	0.00 RPM	9.42 RPM
bodymap2_adrenal	0.02 RPM	13.98 RPM
bodymap2_brain	0.00 RPM	3.98 RPM
bodymap2_breast	0.00 RPM	16.73 RPM
bodymap2_colon	0.27 RPM	15.64 RPM
bodymap2_heart	0.00 RPM	6.85 RPM
bodymap2_kidney	0.00 RPM	24.13 RPM
bodymap2_liver	0.00 RPM	8.89 RPM
bodymap2_lung	0.00 RPM	21.11 RPM
bodymap2_lymph_node	0.00 RPM	16.90 RPM
bodymap2_ovary	0.00 RPM	15.90 RPM
bodymap2_prostate	0.00 RPM	17.48 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.62 RPM
bodymap2_testis	0.00 RPM	22.81 RPM
bodymap2_thyroid	0.06 RPM	12.73 RPM
bodymap2_white_blood_cells	0.00 RPM	35.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1649 was not detected

EST

No EST(s) were mapped for retro_hsap_1649 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_53778	354 libraries	489 libraries	913 libraries	64 libraries	9 libraries

The graphical summary, for retro_hsap_1649 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1649 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1120
Gorilla gorilla	retro_ggor_1245
Pongo abelii	retro_pabe_1400

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.08 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).