RetrogeneDB ID: retro_hsap_2697

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:121213047..121213752(+)
• Located in intron of: ENSG00000051341

Retrocopy information

• Ensembl ID: ENSG00000242445
• 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_2697
TTTGTGAAAAGGCCTAAGAATTTTGGCACTGGACAGGACATCCAGCCCAAAAGAGACCTCACCCGCTTTGTGAAACGGCC
CCGCTATATCAGGTTGCAGCGGCAGAGAGCCATCCTCTATAAGCGGCTGAAAGTGCCTCCTGCGATTAACCAGTTCACCC
AGGCCCTGGACCGCCAAACAGCTACTCAGCTGCTTAAGCTGGCCCACAAGTACAGACCAGAGTCAAGGCAAGAGAAGAAG
CAGAGGCTGTTGGCCTGGGCCAAGAAGAAAGCTGCTGGCAGAGGGGACGTCCCCACCAAGAGACCACCTGTCCTTCGAAC
AGGAGTTAACACCGTCACCACCTTGGTGGAGAACAAGAAAGCTCAGCTGGTGGTGATTGCACACAACGCGGATCCCATCA
AGCTGGCTGTCTTCTTGCCTGCCCTGTGTCGTAAAATGGGGGTCCCTTACTGCATTACCAAGGGGAAGGCAAGACTGGGA
CGTCTAGTCCACAGGAAGACCTGCACCACTGTCGCCTTCACACAGGTGAACTCGGAAGACAAAGGCACTTTGGCTAAGCT
GGTGGAAGTTATCAGGACCAATTACAACGACAGATAGGATGAGACCCACCGTCACTGGGGCGGCAACGTCCTGGGTCCTA
AGTCTGTGGCTCGTATCACCAAGCTCGAAAAGGCAAAGGCTAAAGAACTTGCCACTAAACTGGGT

Alignment

ORF - retro_hsap_2697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 88.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHK
          F.KRPKNFG.GQDIQPKRDLTRFVK.PRYIRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHK
Retrocopy FVKRPKNFGTGQDIQPKRDLTRFVKRPRYIRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHK

Parental  YRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLP
          YRPE..QEKKQRLLA.A.KKAAG.GDVPTKRPPVLR.GVNTVTTLVENKKAQLVVIAH..DPI.L.VFLP
Retrocopy YRPESRQEKKQRLLAWAKKKAAGRGDVPTKRPPVLRTGVNTVTTLVENKKAQLVVIAHNADPIKLAVFLP

Parental  ALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNV
          ALCRKMGVPYCI.KGKARLGRLVHRKTCTTVAFTQVNSEDKG.LAKLVE.IRTNYNDR.DE..RHWGGNV
Retrocopy ALCRKMGVPYCITKGKARLGRLVHRKTCTTVAFTQVNSEDKGTLAKLVEVIRTNYNDR*DETHRHWGGNV

Parental  LGPKSVARIAKLEKAKAKELATKLG
          LGPKSVARI.KLEKAKAKELATKLG
Retrocopy LGPKSVARITKLEKAKAKELATKLG

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	0.06 RPM	0.00 RPM
bodymap2_adrenal	0.23 RPM	0.00 RPM
bodymap2_brain	0.12 RPM	0.00 RPM
bodymap2_breast	0.04 RPM	0.00 RPM
bodymap2_colon	0.21 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.10 RPM	0.00 RPM
bodymap2_liver	0.04 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.00 RPM
bodymap2_ovary	0.12 RPM	0.00 RPM
bodymap2_prostate	0.10 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.13 RPM	0.00 RPM
bodymap2_testis	0.02 RPM	0.00 RPM
bodymap2_thyroid	0.02 RPM	0.00 RPM
bodymap2_white_blood_cells	0.02 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2697 was not detected

EST

No EST(s) were mapped for retro_hsap_2697 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_128091	492 libraries	678 libraries	612 libraries	46 libraries	1 library

The graphical summary, for retro_hsap_2697 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_2697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2697 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1881
Pongo abelii	retro_pabe_2286

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.37 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.35 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.36 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.26 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.21 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.17 RPM
FIN_HG00349	0.34 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.20 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.21 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.17 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.22 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.19 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.26 RPM
TSI_NA20765	0.17 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.21 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.17 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.16 RPM
YRI_NA19114	0.21 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.20 RPM

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Indel association:

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