RetrogeneDB ID: retro_hsap_2878

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:169663698..169664530(-)
• Located in intron of: ENSG00000239219

Retrocopy information

• Ensembl ID: ENSG00000244193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FHL1
• Ensembl ID: ENSG00000022267
• Aliases: FHL1, FHL-1, FHL1A, FHL1B, FLH1A, KYOT, SLIM, SLIM-1, SLIM1, SLIMMER, XMPMA
• Description: four and a half LIM domains 1 [Source:HGNC Symbol;Acc:3702]

Sequence

>retro_hsap_2878
GAAGTTTTTGACTGTCTCTACTGCAGGGACCCCTTGCAGAGGAAAAAGTATGTGCAGAAGGGTGACCACCACTGCTGCCT
GAAATGCTTTGACAGGTTCTGTGCCAACACCTGCGTGGAATGCTGCAAGCCCATCCATGTGGACTCCAAGGAGGTGCACT
ATAAAAACTGCTCCTGGCATGACCCCTGCTTCCACTGTGCCAAGTGCCTTCACCCCTTGCCAATGAGACCTTTGTGGCCA
AGGACAACAAGATCCTGTGCAACAAGTTTGCCACTCAGGAGGACTCTCCCAAGTGTAAGGGGTGCTTCAAGGCCTTTGTG
GCAGGAGATCAAAAATGGAGTACAAGGGGACCATCTCGCACAAAGACCGCTTCACCTGTAGCAACTGCAAGCAAGTCATG
GGGACTGGAAGCTTCTTCTCTAAAGGGAAGGACTTCTACTGTGTGACTTGCCATGAGACCAAGTTTGCTAAGCATTGTGT
GAAGTGCAACAAGGCCATCGCATCTTGGGGAGTCACTTACTAGGATGAGCCCTGGCATGCCGAGGGCTTTGTATGTGTTA
CCTGCTCTAAGAAGCTGGCTGTGCAGCATTTCACCACTGTGGAGGACCAGTAATACTGTGTGGATTGCTACAAGAACTTT
GTGGCCAAGAAGTGTGCTGGATGCAAGCACCCCATCACTGGGTTTGGTAAAGGCTCCAGTGTGGTGGCCTATGAAGGACA
ATCCTGGCACGACTGCTGCTTCCACTGCAAAAAATGCTCTGTGAATCTGGCCAACAAGCACTTTGTTTTCCACGAGGAGC
AAGTATATTGCCCTGACTGTGCCAAAAAGTTG

Alignment

ORF - retro_hsap_2878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85. %
• Parental protein coverage: 93.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKFDCHYCRDPLQGKKYVQKDGHHCCLKCFDKFCANTCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCL
          E.FDC.YCRDPLQ.KKYVQK..HHCCLKCFD.FCANTCVEC.KPI..DSKEVHYKN..WHD.CF.CAKCL
Retrocopy EVFDCLYCRDPLQRKKYVQKGDHHCCLKCFDRFCANTCVECCKPIHVDSKEVHYKNCSWHDPCFHCAKCL

Parental  HPL-ANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQN-VEYKGTVWHKDCFTCSNCKQVIGTGS
          HPL.ANETFVAKDNKILCNK..T.EDSPKCKGCFKA.VAGDQ...EYKGT..HKD.FTCSNCKQV.GTGS
Retrocopy HPL<ANETFVAKDNKILCNKFATQEDSPKCKGCFKAFVAGDQK<MEYKGTISHKDRFTCSNCKQVMGTGS

Parental  FFPKGEDFYCVTCHETKFAKHCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCV
          FF.KG.DFYCVTCHETKFAKHCVKCNKAI.S.G.TY.D.PWHA..FVCVTCSKKLA.Q.FT.VEDQ.YCV
Retrocopy FFSKGKDFYCVTCHETKFAKHCVKCNKAIASWGVTY*DEPWHAEGFVCVTCSKKLAVQHFTTVEDQ*YCV

Parental  DCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL
          DCYKNFVAKKCAGCK.PITGFGKGSSVVAYEGQSWHD.CFHCKKCSVNLANK.FVFH.EQVYCPDCAKKL
Retrocopy DCYKNFVAKKCAGCKHPITGFGKGSSVVAYEGQSWHDCCFHCKKCSVNLANKHFVFHEEQVYCPDCAKKL

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	992.98 RPM
bodymap2_adrenal	0.00 RPM	234.99 RPM
bodymap2_brain	0.09 RPM	122.22 RPM
bodymap2_breast	0.04 RPM	1687.12 RPM
bodymap2_colon	0.00 RPM	686.67 RPM
bodymap2_heart	0.02 RPM	708.74 RPM
bodymap2_kidney	0.00 RPM	66.69 RPM
bodymap2_liver	0.00 RPM	18.61 RPM
bodymap2_lung	0.00 RPM	682.79 RPM
bodymap2_lymph_node	0.33 RPM	201.63 RPM
bodymap2_ovary	0.00 RPM	93.38 RPM
bodymap2_prostate	0.00 RPM	782.44 RPM
bodymap2_skeletal_muscle	0.00 RPM	4525.77 RPM
bodymap2_testis	0.11 RPM	399.86 RPM
bodymap2_thyroid	0.00 RPM	1431.25 RPM
bodymap2_white_blood_cells	0.00 RPM	26.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2878 was not detected

EST

No EST(s) were mapped for retro_hsap_2878 retrocopy.

TSS

No TSS is located nearby retro_hsap_2878 retrocopy 5' end.

Lab

retro_hsap_2878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2878 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1994
Pongo abelii	retro_pabe_2382
Macaca mulatta	retro_mmul_1458

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299, retro_dord_722,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878 ,
Homo sapiens	ENSG00000196923	1 retrocopy	retro_hsap_3940,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.31 RPM
CEU_NA11930	0.95 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.56 RPM
CEU_NA12751	0.22 RPM
CEU_NA12760	0.36 RPM
CEU_NA12827	0.42 RPM
CEU_NA12872	0.24 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.47 RPM
FIN_HG00277	0.22 RPM
FIN_HG00315	0.55 RPM
FIN_HG00321	0.27 RPM
FIN_HG00328	0.24 RPM
FIN_HG00338	0.62 RPM
FIN_HG00349	0.34 RPM
FIN_HG00375	0.51 RPM
FIN_HG00377	0.23 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.19 RPM
GBR_HG00131	0.17 RPM
GBR_HG00133	0.46 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.31 RPM
GBR_HG00143	0.29 RPM
TSI_NA20512	0.17 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.54 RPM
TSI_NA20538	0.55 RPM
TSI_NA20756	0.26 RPM
TSI_NA20765	0.37 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.34 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.48 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.32 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.25 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.90 RPM

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Indel association:

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