RetrogeneDB ID: retro_hsap_4041

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:35382696..35383281(-)
• Located in intron of: ENSG00000156687

Retrocopy information

• Ensembl ID: ENSG00000232024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSG00000161654
• Aliases: LSM12, PNAS-135
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_hsap_4041
ATGGCGGCTCCTCCGGGCGAGTACTTCAGCGTTGGGAGCCAGGTGTCGTGCCGGACGTGCCAGGAGCAGCGGCTGCAGGG
CGAGGTGGTAGCCTTTGACTACCAATCCAAAATGCTGGCTTTAAAATGTCCCTCTTCCAGTGGAAAGCCCAACCATGCAG
ACATCTTGCTCATAAACTTACAGTATGTTTCAGAAGTGGAAATAATTAATGACCGAACAGAAACCCCTCCTCCCCTAGCT
TCACTCAATGTTAGTAAGCTTGCCAGCAAAGCACGGACAGAGAAGGAGGAGAAGCTGAGCCAGGCCTATGCAATCAGTGC
TGGTGTCTCTCTAGAGGGCCAGCAGCTCTTCCAGACCATTCACAAGACCATTAAAGACTGTAAATGGCAAGAAAAAAACA
TCGTAGTCATGGAAGAAGTTGTTATTACACCCCCATATCAAGTGGAAAACTGTAAAGGCAAAGAGGGGAGTGCACTGAGC
CATGTACGCAAAATAGTTGAAAAACATTTTAGAGACGTGGAAAGCCAAAAGATACTGCAACGTTCACAAGCCCAGCAACC
ACAGAAGGAGGCTGCCCTGTCATCC

Alignment

ORF - retro_hsap_4041 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIIN
          MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIIN
Retrocopy MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIIN

Parental  DRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEV
          DRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEV
Retrocopy DRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEV

Parental  VITPPYQVENCKGKEGSALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAALSS
          VITPPYQVENCKGKEGSALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAALSS
Retrocopy VITPPYQVENCKGKEGSALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAALSS

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	1.35 RPM	9.26 RPM
bodymap2_adrenal	1.66 RPM	7.74 RPM
bodymap2_brain	0.63 RPM	4.69 RPM
bodymap2_breast	1.73 RPM	6.52 RPM
bodymap2_colon	0.46 RPM	5.88 RPM
bodymap2_heart	0.78 RPM	6.78 RPM
bodymap2_kidney	0.60 RPM	6.45 RPM
bodymap2_liver	0.76 RPM	7.82 RPM
bodymap2_lung	1.35 RPM	9.58 RPM
bodymap2_lymph_node	1.24 RPM	7.66 RPM
bodymap2_ovary	1.81 RPM	8.85 RPM
bodymap2_prostate	0.48 RPM	7.24 RPM
bodymap2_skeletal_muscle	2.67 RPM	20.21 RPM
bodymap2_testis	2.15 RPM	11.14 RPM
bodymap2_thyroid	1.37 RPM	5.80 RPM
bodymap2_white_blood_cells	1.91 RPM	12.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4041 was not detected

EST

No EST(s) were mapped for retro_hsap_4041 retrocopy.

TSS

No TSS is located nearby retro_hsap_4041 retrocopy 5' end.

Lab

retro_hsap_4041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4041 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041 ,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.01 RPM
CEU_NA11843	0.85 RPM
CEU_NA11930	0.91 RPM
CEU_NA12004	1.14 RPM
CEU_NA12400	0.70 RPM
CEU_NA12751	0.87 RPM
CEU_NA12760	0.94 RPM
CEU_NA12827	1.51 RPM
CEU_NA12872	1.25 RPM
CEU_NA12873	1.05 RPM
FIN_HG00183	0.85 RPM
FIN_HG00277	1.00 RPM
FIN_HG00315	1.08 RPM
FIN_HG00321	0.91 RPM
FIN_HG00328	0.66 RPM
FIN_HG00338	1.09 RPM
FIN_HG00349	1.22 RPM
FIN_HG00375	1.15 RPM
FIN_HG00377	1.13 RPM
FIN_HG00378	1.32 RPM
GBR_HG00099	1.34 RPM
GBR_HG00111	0.47 RPM
GBR_HG00114	1.18 RPM
GBR_HG00119	1.22 RPM
GBR_HG00131	1.06 RPM
GBR_HG00133	0.99 RPM
GBR_HG00134	0.81 RPM
GBR_HG00137	0.99 RPM
GBR_HG00142	1.44 RPM
GBR_HG00143	0.96 RPM
TSI_NA20512	0.65 RPM
TSI_NA20513	1.06 RPM
TSI_NA20518	1.97 RPM
TSI_NA20532	0.95 RPM
TSI_NA20538	1.43 RPM
TSI_NA20756	0.90 RPM
TSI_NA20765	0.87 RPM
TSI_NA20771	0.96 RPM
TSI_NA20786	1.12 RPM
TSI_NA20798	1.22 RPM
YRI_NA18870	1.25 RPM
YRI_NA18907	0.94 RPM
YRI_NA18916	1.05 RPM
YRI_NA19093	1.41 RPM
YRI_NA19099	1.15 RPM
YRI_NA19114	1.47 RPM
YRI_NA19118	1.33 RPM
YRI_NA19213	1.10 RPM
YRI_NA19214	0.93 RPM
YRI_NA19223	0.86 RPM

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Indel association:

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