RetrogeneDB ID: retro_hsap_3969

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:70041903..70042577(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000254332
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSG00000167460
• Aliases: TPM4, HEL-S-108
• Description: tropomyosin 4 [Source:HGNC Symbol;Acc:12013]

Sequence

>retro_hsap_3969
GCGCAGGGCCTGCAGCGGGAGCTGGACGGCAAGCGCGAGTGGCGCGAGAAAGCTGAAGGTGATGTGGCCACCCTCAACCG
ACGCATCCAGCTCGTTGAGGAGGAGTTGGACAGGGCTCAGGAACGACTGGCCACAGCCCTGCAGAAGCTGGAGGAGGCAG
AAAAAGTTGCAGATGAGAGTGAAAGAGGAATGAAGGTGATAGAAAACCGGGCCATGAAGGATGAGGAGAAGATGGAGATT
CAGGAGATGCAGCTCAAAGAGGCCAAGCACATTGCGGAAAAGGCTGACCGCAAATACGAGAAGGTAGCTCGTAAGCTGGT
CATCCTGGAGGGTGAGCTGGAGAGGGCAGAGGAGCGTGCAGAGATGCGTGCGGAGGTGTCCGAACTAAAATGTGGTGACG
TGGCAAAGAACTCAAGAATGTTACTAACAATCTGAAATCGCTGGAAGCTGCATCTGAAAAGTATTCTGAAAAGGAGGACA
AATATGAAGAAGAAATTAAACTTCTGTCTGACAAAGTGAAAGAGGCTGAGACCCGTGCTGAATTTGCAGAGAGAACGGTT
GCAAAACTGGAAAAGACAATTGATGACCTGGAAGAGAAACTTGCCCAGGCCAAAGAAGAGAACGTGGGCTTACATCAGAC
ACTGGATCAGACACTAAACGAACTTAACTGTATA

Alignment

ORF - retro_hsap_3969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.36 %
• Parental protein coverage: 89.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENR
          AQGLQRELDG.RE.REKAEGDVA.LNRRIQLVEEELDRAQERLATALQKLEEAEK.ADESERGMKVIENR
Retrocopy AQGLQRELDGKREWREKAEGDVATLNRRIQLVEEELDRAQERLATALQKLEEAEKVADESERGMKVIENR

Parental  AMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAE----VSELKCGDLE-EELK
          AMKDEEKMEIQEMQLKEAKHIAE.ADRKYE.VARKLVILEGELERAEERAE....VSELKCGD....ELK
Retrocopy AMKDEEKMEIQEMQLKEAKHIAEKADRKYEKVARKLVILEGELERAEERAEMRAEVSELKCGDVA<KELK

Parental  NVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTVAKLEKTIDDLEEKLAQAKEENV
          NVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDK.KEAETRAEFAERTVAKLEKTIDDLEEKLAQAKEENV
Retrocopy NVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKVKEAETRAEFAERTVAKLEKTIDDLEEKLAQAKEENV

Parental  GLHQTLDQTLNELNCI
          GLHQTLDQTLNELNCI
Retrocopy GLHQTLDQTLNELNCI

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	2.92 RPM	717.16 RPM
bodymap2_adrenal	1.82 RPM	529.36 RPM
bodymap2_brain	0.52 RPM	154.12 RPM
bodymap2_breast	1.21 RPM	317.96 RPM
bodymap2_colon	1.89 RPM	542.29 RPM
bodymap2_heart	0.00 RPM	107.68 RPM
bodymap2_kidney	0.52 RPM	295.73 RPM
bodymap2_liver	0.00 RPM	50.80 RPM
bodymap2_lung	0.72 RPM	1591.70 RPM
bodymap2_lymph_node	0.13 RPM	419.69 RPM
bodymap2_ovary	4.18 RPM	886.43 RPM
bodymap2_prostate	0.07 RPM	516.99 RPM
bodymap2_skeletal_muscle	0.00 RPM	56.67 RPM
bodymap2_testis	1.58 RPM	440.37 RPM
bodymap2_thyroid	0.75 RPM	210.46 RPM
bodymap2_white_blood_cells	0.00 RPM	316.50 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3969 was not detected

EST

No EST(s) were mapped for retro_hsap_3969 retrocopy.

TSS

No TSS is located nearby retro_hsap_3969 retrocopy 5' end.

Lab

retro_hsap_3969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3969 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2694
Gorilla gorilla	retro_ggor_2665
Pongo abelii	retro_pabe_3263

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Homo sapiens	ENSG00000167460	2 retrocopies	retro_hsap_2623, retro_hsap_3969 ,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Oryctolagus cuniculus	ENSOCUG00000009884	1 retrocopy	retro_ocun_1652,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.24 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.26 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.27 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.33 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.26 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.23 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.19 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.67 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.38 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.26 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.21 RPM
YRI_NA18916	0.11 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.40 RPM
YRI_NA19114	0.31 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.26 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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