RetrogeneDB ID: retro_hsap_3766

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:102395592..102396383(+)
• Located in intron of: ENSG00000222011

Retrocopy information

• Ensembl ID: ENSG00000213385
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL7A
• Ensembl ID: ENSG00000260501
• Aliases: None
• Description: ribosomal protein L7a [Source:HGNC Symbol;Acc:10364]

Sequence

>retro_hsap_3766
ATGCCGAAAGGAAAGGAGGCCAAGGGGAAGAAGTTGGCTCTGGCCCCTGCTTTTGTGAAGAAGCAGGAGGCCAAGAAAGT
GGTGAATCCCCTGTTTGAGAAAAGGCCTAAGAATTTTGGCATTGGACAGGACATCCAGCCCAAAAGAGACCTCACCTGCT
TTGTGAAATGGCCCCGCTATATCAGGTTGCAATGGCAGAGATCCATACTCTATAAGCAGCTGAAAGTGCCTCCTGCGATT
AACCAGTTCACCCAGGCCCTGGAAGGCCAAACAGCTACTCAGCTGCTTAAGCTGGCCCACAAATACAGACCAGAGACAAA
GCAAGAGAAGAAGCGGAGGCTGTTGGCCCAGGCAGAGTTGTGGGCAAAGGGGACCTCCCCATTAAGAGACCACCTGTCTT
TCGAGCAGGAGTTAACACCATCACCACCTTTGTGGATAACAAGAAAGCTCCGCTGGTGGTGACTGCACACGACATGGATC
CCATTGAGCTGACTGTTTTCCTGCCTGTCCTGTGTCATAAAATGGGAGCCACTTGCTGCATTATCAAGGGGAAGGCAAGA
CTGGGATGTCTAGTTCACAGGAAGACCTACACCACTGTCGACTTCACACAGGTTAACTCAGAAGACAAAGGAGCTTTGGC
TAAGCTGATGGAAGCTATCGGGACCAATTACAATGCCAGATACGATGAGACCCACTGTCACTGGGACGGCAATGTCCTGG
GTCCCAAGTCTGTGGCTCACATTGCCAAGCTCGAAAAGGCAAAGGCTAAAGAACTTGCCACTAAACTGGGT

Alignment

ORF - retro_hsap_3766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAIL
          MPKGK.AKGKK.A.APA.VKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLT.FVKWPRYIRLQ.QR.IL
Retrocopy MPKGKEAKGKKLALAPAFVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTCFVKWPRYIRLQWQRSIL

Parental  YKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTK-RPPVLRAG
          YK.LKVPPAINQFTQAL..QTATQLLKLAHKYRPETKQEKK.RLLA.AE..A..KG..P...RPPV.RAG
Retrocopy YKQLKVPPAINQFTQALEGQTATQLLKLAHKYRPETKQEKKRRLLAQAELWA--KGTSPLR<RPPVFRAG

Parental  VNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNS
          VNT.TT.V.NKKA.LVV.AHD.DPIEL.VFLP.LC.KMG...CIIKGKARLG.LVHRKT.TTV.FTQVNS
Retrocopy VNTITTFVDNKKAPLVVTAHDMDPIELTVFLPVLCHKMGATCCIIKGKARLGCLVHRKTYTTVDFTQVNS

Parental  EDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG
          EDKGALAKL.EAI.TNYN.RYDE...HW.GNVLGPKSVA.IAKLEKAKAKELATKLG
Retrocopy EDKGALAKLMEAIGTNYNARYDETHCHWDGNVLGPKSVAHIAKLEKAKAKELATKLG

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	0.04 RPM	0.00 RPM
bodymap2_adrenal	0.29 RPM	0.00 RPM
bodymap2_brain	0.05 RPM	0.00 RPM
bodymap2_breast	0.08 RPM	0.00 RPM
bodymap2_colon	0.04 RPM	0.00 RPM
bodymap2_heart	0.04 RPM	0.00 RPM
bodymap2_kidney	0.23 RPM	0.00 RPM
bodymap2_liver	0.08 RPM	0.00 RPM
bodymap2_lung	0.14 RPM	0.00 RPM
bodymap2_lymph_node	0.13 RPM	0.00 RPM
bodymap2_ovary	0.13 RPM	0.00 RPM
bodymap2_prostate	0.03 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.15 RPM	0.00 RPM
bodymap2_testis	0.06 RPM	0.00 RPM
bodymap2_thyroid	0.15 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_3766 was not detected

EST

No EST(s) were mapped for retro_hsap_3766 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_169098	1096 libraries	100 libraries	536 libraries	84 libraries	13 libraries

The graphical summary, for retro_hsap_3766 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_3766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3766 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000260501	36 retrocopies	retro_hsap_1031, retro_hsap_1103, retro_hsap_1157, retro_hsap_1327, retro_hsap_1340, retro_hsap_1402, retro_hsap_1435, retro_hsap_1565, retro_hsap_1656, retro_hsap_1936, retro_hsap_1937, retro_hsap_2016, retro_hsap_2172, retro_hsap_218, retro_hsap_2476, retro_hsap_261, retro_hsap_2697, retro_hsap_2806, retro_hsap_2893, retro_hsap_2931, retro_hsap_297, retro_hsap_3060, retro_hsap_3572, retro_hsap_3603, retro_hsap_3749, retro_hsap_3766 , retro_hsap_377, retro_hsap_3873, retro_hsap_3877, retro_hsap_4135, retro_hsap_4141, retro_hsap_612, retro_hsap_660, retro_hsap_750, retro_hsap_767, retro_hsap_771,