RetrogeneDB ID: retro_hsap_3865

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:65970644..65971210(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000179342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNA11
• Ensembl ID: ENSG00000088256
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), alpha 11 (Gq class) [Source:HGNC Symbol;Acc:4379]

Sequence

>retro_hsap_3865
ATGACTCTGGAGTCCATGATGGCGTGTTGCCTGAGCGATAAGGTGAAGGAGTCCAAGCGGATCAACGCCGAGATCCAGAA
GCAGCTGCGGGGGACAAGCGCGACGCCCGGCGCCAGCTCAAGCTGCTGCTGCTCCTCACGGGCGAGAGCGGGAAGAGCAC
CTTCATCAAGCAGATGCGCATCATCCATGGCGCCGGGTACTAGGAGGAGGACAAAAGGGGCTTCACCAAGCTCGTCTACC
AGAACATTTTCACCGCCATGCAGGCCATGATCCGGGCCATGGAGACGCTGAAGATCCTCTACAAGTTGGAGCAGAACAAG
GCCAATGCGCTCCAGATCCGAGAGGTGGACGTGGAGAAGGTGACCACCTTTGAGCATCGGTACGTCAGCGCCATCAAGAC
CCTGTGGGACGACCCCGGCATCCACGAGTGCTACGACCGCAGGCGCGAGTACCAGCTCTCGGACTCGGCCAAGTACTGCG
TGACCGACGTAGACTGCATCGCCACCTCGAGCTACCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACC
GGCGTC

Alignment

ORF - retro_hsap_3865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.53 %
• Parental protein coverage: 52.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTLESMMACCLSDEVKESKRINAEIEKQLRR-DKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSE
          MTLESMMACCLSD.VKESKRINAEI.KQLR..DKRDARR.LKLLLL.TGESGKSTFIKQMRIIHGAGY.E
Retrocopy MTLESMMACCLSDKVKESKRINAEIQKQLRG<DKRDARRQLKLLLLLTGESGKSTFIKQMRIIHGAGY*E

Parental  EDKRGFTKLVYQNIFTAMQAMIRAMETLKILYKYEQNKANALLIREVDVEKVTTFEHQYVSAIKTLWEDP
          EDKRGFTKLVYQNIFTAMQAMIRAMETLKILYK.EQNKANAL.IREVDVEKVTTFEH.YVSAIKTLW.DP
Retrocopy EDKRGFTKLVYQNIFTAMQAMIRAMETLKILYKLEQNKANALQIREVDVEKVTTFEHRYVSAIKTLWDDP

Parental  GIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGI
          GI.ECYDRRREYQLSDSAKY..TDVD.IAT..YLPTQQDVLRVRVPTTG.
Retrocopy GIHECYDRRREYQLSDSAKYCVTDVDCIATSSYLPTQQDVLRVRVPTTGV

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	74.42 RPM
bodymap2_adrenal	0.06 RPM	42.23 RPM
bodymap2_brain	0.05 RPM	28.85 RPM
bodymap2_breast	0.12 RPM	52.63 RPM
bodymap2_colon	0.06 RPM	52.71 RPM
bodymap2_heart	0.02 RPM	36.92 RPM
bodymap2_kidney	0.00 RPM	38.47 RPM
bodymap2_liver	0.00 RPM	16.41 RPM
bodymap2_lung	0.00 RPM	40.77 RPM
bodymap2_lymph_node	0.00 RPM	25.07 RPM
bodymap2_ovary	0.10 RPM	56.13 RPM
bodymap2_prostate	0.00 RPM	51.67 RPM
bodymap2_skeletal_muscle	0.00 RPM	52.11 RPM
bodymap2_testis	0.09 RPM	76.22 RPM
bodymap2_thyroid	0.00 RPM	53.86 RPM
bodymap2_white_blood_cells	0.00 RPM	2.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3865 was not detected

EST

No EST(s) were mapped for retro_hsap_3865 retrocopy.

TSS

No TSS is located nearby retro_hsap_3865 retrocopy 5' end.

Lab

retro_hsap_3865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088256	1 retrocopy	retro_hsap_3865 ,
Gorilla gorilla	ENSGGOG00000014995	3 retrocopies	retro_ggor_1760, retro_ggor_2603, retro_ggor_2604,
Macaca mulatta	ENSMMUG00000002961	1 retrocopy	retro_mmul_1605,
Pongo abelii	ENSPPYG00000009366	1 retrocopy	retro_pabe_3045,