RetrogeneDB ID: retro_hsap_4108

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:107709703..107710268(-)
• Located in intron of: ENSG00000164830

Retrocopy information

• Ensembl ID: ENSG00000253676
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSG00000158710
• Aliases: TAGLN2, HA1756
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_hsap_4108
TCCCCGCAGCCACCGCCACCCATTGGAATGGCCAACAGGGGACCTGCATTATGGCCTGAGCCAGGAGGTGCAGCAGAAGA
TTGAGAAACAGTATGATGCAGATCTGGAGCAGATCCTGATCCAGTGGATCACCACCCAGTGCCGAAAGGATGTGGGCCGG
TCCCAGCCTGGACGCGAGAACTTCCAGAACTGGCTCAAGGATGGCACGGTGTTATGTGAGCTCAATAATGCACTGTACCC
CAAGGGGCAGGTCCCAGTAAAGAAGATCCAGGCCTCCACCATGGCCTTCAAGCAGATGGAGAAGATCTCTCAGTTCCTGC
AAGCAGCTGAGCGCTATGGCATTAACACCACTGACATCTTCCAAACTGTGGACCTCTGGGAAGGAAAGAACATGGCCTGT
GTGCAGCGGACGCTGAGGAATCTGGGTGGGTTGGCAGTAGCCTGGGATGATGGGCTCTTCTCTGGGGATCCCAACTGGTT
CCCTAAGAAATCCAAGGAGAATCCTCGGAACTTCTCGGATAACCAGCTGCAAGAGGGCAAGAACGTGATCGGGCTACAGA
TGGGG

Alignment

ORF - retro_hsap_4108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 85.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPQPPPPIGMANRGPA-YGLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGRPQPGRENFQNWLKDGT
          SPQPPPPIGMANRGPA.YGLS.EVQQKIEKQYDADLEQILIQWITTQCRKDVGR.QPGRENFQNWLKDGT
Retrocopy SPQPPPPIGMANRGPA>YGLSQEVQQKIEKQYDADLEQILIQWITTQCRKDVGRSQPGRENFQNWLKDGT

Parental  VLCELINALYPEGQAPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTLM
          VLCEL.NALYP.GQ.PVKKIQASTMAFKQME.ISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTL.
Retrocopy VLCELNNALYPKGQVPVKKIQASTMAFKQMEKISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTLR

Parental  NLGGLAVARDDGLFSGDPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMG
          NLGGLAVA.DDGLFSGDPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMG
Retrocopy NLGGLAVAWDDGLFSGDPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMG

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	0.10 RPM	206.75 RPM
bodymap2_adrenal	0.33 RPM	217.49 RPM
bodymap2_brain	0.00 RPM	28.83 RPM
bodymap2_breast	0.12 RPM	144.11 RPM
bodymap2_colon	0.08 RPM	198.75 RPM
bodymap2_heart	0.02 RPM	72.22 RPM
bodymap2_kidney	0.10 RPM	166.19 RPM
bodymap2_liver	0.00 RPM	67.98 RPM
bodymap2_lung	0.21 RPM	750.90 RPM
bodymap2_lymph_node	0.00 RPM	234.94 RPM
bodymap2_ovary	0.04 RPM	101.72 RPM
bodymap2_prostate	0.02 RPM	180.80 RPM
bodymap2_skeletal_muscle	0.02 RPM	27.86 RPM
bodymap2_testis	0.02 RPM	93.89 RPM
bodymap2_thyroid	0.02 RPM	68.53 RPM
bodymap2_white_blood_cells	0.18 RPM	652.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4108 was not detected

EST

No EST(s) were mapped for retro_hsap_4108 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_179628	49 libraries	29 libraries	181 libraries	233 libraries	1337 libraries

The graphical summary, for retro_hsap_4108 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_4108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4108 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2788

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Homo sapiens	ENSG00000064666	16 retrocopies	retro_hsap_1168, retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257, retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108 ,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.17 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.21 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.27 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.36 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.33 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.23 RPM
FIN_HG00378	0.28 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.17 RPM
GBR_HG00114	0.16 RPM
GBR_HG00119	0.19 RPM
GBR_HG00131	0.34 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.20 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.25 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.39 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.38 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.16 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.17 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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