RetrogeneDB ID: retro_hsap_4926

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: Y:20309769..20310891(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000229465
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSG00000267807
• Aliases: None
• Description: actin, gamma 1 [Source:HGNC Symbol;Acc:144]

Sequence

>retro_hsap_4926
GTAGAAGAAGAGATCGCTGCGCTCGTCATTGACAATGGCTCTTGCATGTGCAAAGCTGGCTTTGCAGGGGACGATGCTCC
CCAAGCCATGTTTCCCTCCACCGTTGGGTTCCCCGGACACCAGGGCGTGATGGTGGACATGGGCCAGAAGGACTCCTACG
TGGGCAATGAAGCCCAGAGCAAGCGCAGCATTCTGACGCTGAAGTACCCCATCAAGCATGGCATCATCACCAACTGGGAC
AACATGGAGAAGATCTGGCACCACTTCTACAATGAGCTGCATGGGGCCCCGGAGTAGCAGCCAGTGCTGCTGACCGAGGA
CCCACTGAACCCCAAGGACAACAGAGAGAAAATGACTCAGATTATGTTTGAGACCTTCAATACCCCGGCCATGTACGTGG
CCATCCGGGATGTGCTGTCCCTCTATGCCTTTGGGCGCACCACTGGCATTGTCATGGACTGTGGACACAGGGTCACCCAC
ACGGTGCCCATCTACGAGGGCTACTCCCTTCCCCATGCCATCCTGCATCTGGACCTGACTGGCTGGGACTTGACTGAGTA
CCTCAAGAAGATCCTCAAGGAGAGAGGCTACAGCTTCACCAACACAGCCCAGCGGGAAATCATGCGCGATATCAAGGAGA
AGCTGTGCTAGGTCTCCCTGGACTTCAAGCAGGAGATGGCCACCCCTGCATCCTCCTCTTCTCTGGAGAAGAGCTATGAA
CTGCCCGATGGCCAGGTCATCACCATTGGCAATGAGTGGTTCTGGTGTCCGGAGGTGCTGTTCCAGCCTTCCTTCCCGTG
CATGGAATCTTGCCGCATCCACCAGACCACCATCAACTCCATCAAGAAGTGTGACGTGGACATCCGCAAAGACCTATACA
CCAATACGGTACTATCCGGTGGCACCACCATGTATCCAGGCATTGCTGACAGGATGCAGAAGGAGATCACTGCCTTGGCG
CCCAGCACCATGAAGATTAAGATCATTGCACCCCCAGAGCGCAAGTTCTCAGTGTGGATCGGTTGCTCCATCCTGAACTC
ACTGGTCACCTTCCAGCAGACATGGATTAGCAAGCAGGAGTATGATGAGTCAGGCCCCTACATCGTCCACCACAAATGCT
TC

Alignment

ORF - retro_hsap_4926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          .EEEIAALVIDNGS.MCKAGFAGDDAP.A.FPS.VG.P.HQGVMV.MGQKDSYVG.EAQSKR.ILTLKYP
Retrocopy VEEEIAALVIDNGSCMCKAGFAGDDAPQAMFPSTVGFPGHQGVMVDMGQKDSYVGNEAQSKRSILTLKYP

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
          I.HGI.TNWD.MEKIWHH.FYNEL..APE..PVLLTE.PLNPK.NREKMTQIMFETFNTPAMYVAI..VL
Retrocopy IKHGIITNWDNMEKIWHH-FYNELHGAPE*QPVLLTEDPLNPKDNREKMTQIMFETFNTPAMYVAIRDVL

Parental  SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          SLYA.GRTTGIVMD.G..VTHTVPIYEGY.LPHAIL.LDL.G.DLT.YL.KIL.ERGYSFT.TA.REI.R
Retrocopy SLYAFGRTTGIVMDCGHRVTHTVPIYEGYSLPHAILHLDLTGWDLTEYLKKILKERGYSFTNTAQREIMR

Parental  DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
          DIKEKLC.V.LDF.QEMAT.ASSSSLEKSYELPDGQVITIGNE.F.CPE.LFQPSF..MESC.IH.TT.N
Retrocopy DIKEKLC*VSLDFKQEMATPASSSSLEKSYELPDGQVITIGNEWFWCPEVLFQPSFPCMESCRIHQTTIN

Parental  SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SI.KCDVDIRKDLY.NTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERK.SVWIG.SIL.SL.
Retrocopy SIKKCDVDIRKDLYTNTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKFSVWIGCSILNSLV

Parental  TFQQMWISKQEYDESGPSIVHRKCF
          TFQQ.WISKQEYDESGP.IVH.KCF
Retrocopy TFQQTWISKQEYDESGPYIVHHKCF

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	0.00 RPM
bodymap2_adrenal	0.00 RPM	0.00 RPM
bodymap2_brain	0.00 RPM	0.00 RPM
bodymap2_breast	0.00 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.00 RPM	0.00 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.00 RPM
bodymap2_ovary	0.00 RPM	0.00 RPM
bodymap2_prostate	0.00 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.02 RPM	0.00 RPM
bodymap2_thyroid	0.00 RPM	0.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4926 was not detected

EST

No EST(s) were mapped for retro_hsap_4926 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_201686	1375 libraries	138 libraries	237 libraries	49 libraries	30 libraries

The graphical summary, for retro_hsap_4926 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_4926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4926 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4935
Pan troglodytes	retro_ptro_3287
Pan troglodytes	retro_ptro_3302
Pan troglodytes	retro_ptro_3292
Pan troglodytes	retro_ptro_3307
Pan troglodytes	retro_ptro_3282

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000267807	2 retrocopies	retro_hsap_1689, retro_hsap_4926 ,