RetrogeneDB ID: retro_hsap_4311

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:127730575..127731136(-)
• Located in intron of: ENSG00000173611

Retrocopy information

• Ensembl ID: ENSG00000177736
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSG00000165060
• Aliases: FXN, CyaY, FA, FARR, FRDA, X25
• Description: frataxin [Source:HGNC Symbol;Acc:3951]

Sequence

>retro_hsap_4311
CTCACCTGGGCCCTGCGGCCAGCAGAATTGGCCCCGCTCTATGGCTGCTGGGGCCTGCGCACTGGAATCGCCGTGGCCTG
CGCACCCCACCATGCCAGTTTGAACCTCCATGGCCTCAACCAGATTCGGAATGTCAAAAAGCAGAGTGTCTATTTGATGA
ATTTGAGGAAATCGGGAACTTTGGGCCACCCAGGCTCTGTAGATGAGACCACCTATGAAAGACTAGCGGAGGAATCACTG
GACTCTTTAGCAGAGTTTTTTGAAGACCTTGCAGACAAGCCATACACGTTTGAGGACTATGATGTTTCCTTTGGGAGTGG
TGTCTTAACTGGTAAACTGGGTAGAGATCTAGCAACCTACGTGATCAACAAGCAGACACCAAACAAGCAAATCTGGTTAT
CTTCTCCATCCAGTGGACTCAAGCGTTATGACTGGACTGAGAAAAACTGGGTGTACTCCCACGATTGCGTGTCCCTCCAT
GATGTGCTCGCTGCAGAGCTCACTAAAGCCTTAAAAACCAAACTGGACTTGTCTTCCTTGGCCTATTCTGGAGAAGACGC
T

Alignment

ORF - retro_hsap_4311 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 89.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTRVPRPAELAPLCGRRGLRTDIDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDET
          LT...RPAELAPL.G..GLRT.I...C.P..AS.N..GLNQI.NVKKQSVYLMNLRKSGTLGHPGS.DET
Retrocopy LTWALRPAELAPLYGCWGLRTGIAVACAPHHASLNLHGLNQIRNVKKQSVYLMNLRKSGTLGHPGSVDET

Parental  TYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGP
          TYERLAEE.LDSLAEFFEDLADKPYTFEDYDVSFGSGVLT.KLG.DL.TYVINKQTPNKQIWLSSPSSG.
Retrocopy TYERLAEESLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTGKLGRDLATYVINKQTPNKQIWLSSPSSGL

Parental  KRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGKDA
          KRYDWT.KNWVYSHD.VSLH..LAAELTKALKTKLDLSSLAYSG.DA
Retrocopy KRYDWTEKNWVYSHDCVSLHDVLAAELTKALKTKLDLSSLAYSGEDA

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	4.33 RPM
bodymap2_adrenal	0.00 RPM	11.16 RPM
bodymap2_brain	0.00 RPM	5.53 RPM
bodymap2_breast	0.04 RPM	8.33 RPM
bodymap2_colon	0.10 RPM	6.03 RPM
bodymap2_heart	0.00 RPM	19.29 RPM
bodymap2_kidney	0.00 RPM	7.26 RPM
bodymap2_liver	0.00 RPM	23.85 RPM
bodymap2_lung	0.00 RPM	3.67 RPM
bodymap2_lymph_node	0.00 RPM	9.12 RPM
bodymap2_ovary	0.02 RPM	15.63 RPM
bodymap2_prostate	0.00 RPM	15.54 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.82 RPM
bodymap2_testis	0.19 RPM	10.90 RPM
bodymap2_thyroid	0.00 RPM	6.95 RPM
bodymap2_white_blood_cells	0.00 RPM	12.72 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4311 was not detected

EST

No EST(s) were mapped for retro_hsap_4311 retrocopy.

TSS

No TSS is located nearby retro_hsap_4311 retrocopy 5' end.

Lab

retro_hsap_4311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939, retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311 ,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203, retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175, retro_ttru_546, retro_ttru_831,