RetrogeneDB ID: retro_hsap_936

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:123006630..123007082(-)
• Located in intron of: ENSG00000166250

Retrocopy information

• Ensembl ID: ENSG00000255342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSG00000069509
• Aliases: None
• Description: FUN14 domain containing 1 [Source:HGNC Symbol;Acc:28746]

Sequence

>retro_hsap_936
AACCCGGCTCCCCAAGAATATGAAAGTGAGGACGACTCTTACGAAGTGTTGGATTTAACTGAGTATGCGCGAAGACACCA
GTGGTGGAATCCAGTGTTTGGCCACAGTTCGGGATCTATGGTGGAAAAATACGCAGTAGCTACCCAGATTGTAATGGGTG
GTGTTCCTGGCTGGTTTGCAGGATTTTTGTTCCAGAAAGTTTGAAAACTTGCAGCAACTGCAGTAGGTGGTGACTTTCTT
GCCGTCAGATTGCTAGTCATAGTGGCTACGTGCAGATTAACTGGAAGAGAGTTGAAAAAGATTCAAACAAAGCAAAAAGG
CAGATGAAGAAACGAGCGAACAAAGCAGCACCGGAAATCAACAATTTAATTGAAGAAGCAATAGAATTTATCAAGCAGCA
CATTGTGATACCCGGTAGATTTGTGGGAGGCTTTTTGCTCGGACTTGCATCT

Alignment

ORF - retro_hsap_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPPPQDYESDDDSYEVLDLTEYARRHQWWNRVFGHSSGPMVEKYSVATQIVMGGVTGWCAGFLFQKVGKL
          NP.PQ.YES.DDSYEVLDLTEYARRHQWWN.VFGHSSG.MVEKY.VATQIVMGGV.GW.AGFLFQKV.KL
Retrocopy NPAPQEYESEDDSYEVLDLTEYARRHQWWNPVFGHSSGSMVEKYAVATQIVMGGVPGWFAGFLFQKV*KL

Parental  AATAVGGGFLLL-QIASHSGYVQIDWKRVEKDVNKAKRQIKKRANKAAPEINNLIEEATEFIKQNIVISS
          AATAVGG.FL...QIASHSGYVQI.WKRVEKD.NKAKRQ.KKRANKAAPEINNLIEEA.EFIKQ.IVI..
Retrocopy AATAVGGDFLAV<QIASHSGYVQINWKRVEKDSNKAKRQMKKRANKAAPEINNLIEEAIEFIKQHIVIPG

Parental  GFVGGFLLGLAS
          .FVGGFLLGLAS
Retrocopy RFVGGFLLGLAS

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	0.12 RPM	5.63 RPM
bodymap2_adrenal	0.06 RPM	10.56 RPM
bodymap2_brain	0.00 RPM	24.52 RPM
bodymap2_breast	0.35 RPM	9.98 RPM
bodymap2_colon	0.00 RPM	9.15 RPM
bodymap2_heart	0.06 RPM	11.43 RPM
bodymap2_kidney	0.00 RPM	15.53 RPM
bodymap2_liver	0.00 RPM	2.98 RPM
bodymap2_lung	0.00 RPM	5.08 RPM
bodymap2_lymph_node	0.00 RPM	3.82 RPM
bodymap2_ovary	0.27 RPM	14.82 RPM
bodymap2_prostate	0.00 RPM	9.28 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.91 RPM
bodymap2_testis	0.09 RPM	19.40 RPM
bodymap2_thyroid	0.00 RPM	15.23 RPM
bodymap2_white_blood_cells	0.00 RPM	8.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_936 was not detected

EST

No EST(s) were mapped for retro_hsap_936 retrocopy.

TSS

No TSS is located nearby retro_hsap_936 retrocopy 5' end.

Lab

retro_hsap_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_936 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_755
Pongo abelii	retro_pabe_806

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010876	1 retrocopy	retro_cjac_896,
Cavia porcellus	ENSCPOG00000012962	2 retrocopies	retro_cpor_507, retro_cpor_508,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Homo sapiens	ENSG00000069509	1 retrocopy	retro_hsap_936 ,
Homo sapiens	ENSG00000165775	3 retrocopies	retro_hsap_2122, retro_hsap_2560, retro_hsap_3530,
Gorilla gorilla	ENSGGOG00000023311	1 retrocopy	retro_ggor_755,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Microcebus murinus	ENSMICG00000000450	2 retrocopies	retro_mmur_1189, retro_mmur_1461,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Nomascus leucogenys	ENSNLEG00000002513	2 retrocopies	retro_nleu_2760, retro_nleu_294,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pongo abelii	ENSPPYG00000020268	2 retrocopies	retro_pabe_806, retro_pabe_829,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 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	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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