RetrogeneDB ID: retro_hsap_377

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:46116710..46117498(-)
• Located in intron of: ENSG00000159592

Retrocopy information

• Ensembl ID: ENSG00000234329
• 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_377
ATGCCGAAAGGAAAGAAGGGCAAGGGGAAGAAGTTGGCTCTGGCCCCTGCTGTCGTCAAGAAGCAGAGCCAAGAAAGTGG
TGAATCCGCTATTTAAGAAAAGGCCTAAGAATTTTGGCATTGGACAGGACACCCAGCCCAAAAGAGACCTCACCTGCTTT
GTGAAATGGCCCTGCTATATCAGGTTGCAGCAGCAGAGAGCCATCCTCTATATGCAGCTGAAAATGCCTCCTGCGATTAA
CCAGTTCATCCAGGCCTTGCGCTGCCAAACAGCTACTCAGCTACTTAAGCTGGCCCACAAGTACAGATCAGAGGCAAAGC
AAGAGAAAGAAGCAGAGGCTATTGGCCCAGGCTGAGAAGAAAGCTGCCAGCAAAGGGGATGTCCCCAGTAAGAGACCACC
TGTCTTTCAAGCAGGAGTCAGCACTTCACCACCTTGGTGGAGAACACGAAGACTCAGCTAGTGGTGATTGCATATGACAT
GGATCCCATCAAGCTGGTTGTCTTCCTACCTGCCCTGTGTCGTAAAATGGGGGTCCCTTACTGCATTATCAAGGGGAAGT
CAAGAGTGGGATGTCTACTCCACAGAAAGACCTGCACCACTGGTTGCCTTCACACAGGTTAACTTGGAAGACAAAGGAGG
TTTGTCTAAGCTGGTGGAAGCTATCAGGATCAATTACAATGACAGATACGATGAGATCTGCCATCACTGGGGAGGCAATG
TCCTGGGTCCCAAGTCTGTGACTCGCATTGCCAAGCTCAAAAAGGCAAAGGCTAAAGAACTTGCCACC

Alignment

ORF - retro_hsap_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 98.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPKGKKAKGKKVAPAPAVVKKQE-AKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAI
          MPKGKK.KGKK.A.APA.V.K...AKKVVNPLF.KRPKNFGIGQD.QPKRDLT.FVKWP.YIRLQ.QRAI
Retrocopy MPKGKKGKGKKLALAPA-VVKKQ>AKKVVNPLFKKRPKNFGIGQDTQPKRDLTCFVKWPCYIRLQQQRAI

Parental  LYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEK-KQRLLARAEKKAAGKGDVPTKRPPVLRA
          LY..LK.PPAINQF.QAL..QTATQLLKLAHKYR.E.KQEK.KQRLLA.AEKKAA.KGDVP.KRPPV..A
Retrocopy LYMQLKMPPAINQFIQALRCQTATQLLKLAHKYRSEAKQEK>KQRLLAQAEKKAASKGDVPSKRPPVFQA

Parental  GVNT-VTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTT-VAFTQ
          GV.T..TTLVEN.K.QLVVIA.D.DPI.LVVFLPALCRKMGVPYCIIKGK.R.G.L.HRKTCTT.VAFTQ
Retrocopy GVST<FTTLVENTKTQLVVIAYDMDPIKLVVFLPALCRKMGVPYCIIKGKSRVGCLLHRKTCTT>VAFTQ

Parental  VNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELAT
          VN.EDKG.L.KLVEAIR.NYNDRYDEI..HWGGNVLGPKSV.RIAKL.KAKAKELAT
Retrocopy VNLEDKGGLSKLVEAIRINYNDRYDEICHHWGGNVLGPKSVTRIAKLKKAKAKELAT

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	0.48 RPM	0.00 RPM
bodymap2_adrenal	0.76 RPM	0.00 RPM
bodymap2_brain	0.30 RPM	0.00 RPM
bodymap2_breast	0.51 RPM	0.00 RPM
bodymap2_colon	0.77 RPM	0.00 RPM
bodymap2_heart	0.35 RPM	0.00 RPM
bodymap2_kidney	0.77 RPM	0.00 RPM
bodymap2_liver	0.27 RPM	0.00 RPM
bodymap2_lung	0.35 RPM	0.00 RPM
bodymap2_lymph_node	1.13 RPM	0.00 RPM
bodymap2_ovary	0.37 RPM	0.00 RPM
bodymap2_prostate	0.12 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.51 RPM	0.00 RPM
bodymap2_thyroid	0.60 RPM	0.00 RPM
bodymap2_white_blood_cells	0.79 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_377 was not detected

EST

No EST(s) were mapped for retro_hsap_377 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_94929	501 libraries	757 libraries	555 libraries	15 libraries	1 library

The graphical summary, for retro_hsap_377 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_377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_377 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_386
Pongo abelii	retro_pabe_330

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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,