RetrogeneDB ID: retro_hsap_218

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:146695143..146695942(+)
• Located in intron of: ENSG00000237188

Retrocopy information

• Ensembl ID: ENSG00000236806
• 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_218
ATGCCAATAGGAAAGAAGGCTAAGGGAAAGAAGGCGGCCCCCGCCCCTGCTATCAGTGAAGAAGCAGGAAGCCAAAAAAG
TTGTGAATCCTCTGTTTGAGAAAAAGCCTAAGAATTTTGGCATTGGACAGGACATACAGCCCCAAAGAGACCTCACCCTC
TTTGTCAGATGGCCCCCCTATATCAGGTTGCAGCAGCAAAGAGCTATCCTTTTATAAGCTGCTGAAAGCACTTCCTGCCA
TTAACCAGTTCACCCAGGCTTCGCACTGCCAAACAGCTACTGACTGCTTACGCGGGCCCACAAGCACAGACCAGAGACAA
AACAAGAGAAGAAGCAGAGACTGTTGTCCTGGACTGAGAAGAAAGCTGCTAGCAAAGGGGATACCCCCATCGAGACACCA
CCCGTCTTTCCAGCAGGGGTTAACACAATCACCACCTTGGTGGAGAACAAGAAGACTCAGCTGGTGGTGATTGCACACGA
TGCGGATCCCATCGAGCTGGTTGTCTTCCTGCCTGCCCTGTGTCCCAAAATGGGGGTCCCTTACTGCATTATCAAGGGTG
AGGTAAGATTGGGATGTCTAGTCCACAGGAAGACCTGCACGACGTTGCCTTCACACAGGTTCACTAGGAAGACAAAGGAG
GTGTGGCTAAGTTGGTGGCAGTTTTCAGAACCAATTACATGGACAGATATGATGAGATTCGCTGCCAATGGGGAGGCAAT
GTCCTGGGTCCTAAATCTGTGGGTTTGAATCACCAAAGTGGAAAAGGGAAAGGTGAAAGAAGTTGCCACTAAACTGGGT

Alignment

ORF - retro_hsap_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPKGKKAKGKKVAPAPAV-VKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAI
          MP.GKKAKGKK.APAPA..VKKQEAKKVVNPLFEK.PKNFGIGQDIQP.RDLT.FV.WP.YIRLQ.QRAI
Retrocopy MPIGKKAKGKKAAPAPAI>VKKQEAKKVVNPLFEKKPKNFGIGQDIQPQRDLTLFVRWPPYIRLQQQRAI

Parental  L-YKRLKVPPAINQFTQALDRQTATQ-LLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLR
          L.YK.LK..PAINQFTQA...QTAT..LL..AHK.RPETKQEKKQRLL...EKKAA.KGD.P...PPV..
Retrocopy L>YKLLKALPAINQFTQASHCQTATD<LLTRAHKHRPETKQEKKQRLLSWTEKKAASKGDTPIETPPVFP

Parental  AGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTT-VAFTQ
          AGVNT.TTLVENKK.QLVVIAHD.DPIELVVFLPALC.KMGVPYCIIKG..RLG.LVHRKTCTT.VAFTQ
Retrocopy AGVNTITTLVENKKTQLVVIAHDADPIELVVFLPALCPKMGVPYCIIKGEVRLGCLVHRKTCTT<VAFTQ

Parental  VNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVAR-IAKLEKAKAKELATKLG
          V..EDKG..AKLV...RTNY.DRYDEIR..WGGNVLGPKSV...I.K.EK.K.KE.ATKLG
Retrocopy VH*EDKGGVAKLVAVFRTNYMDRYDEIRCQWGGNVLGPKSVGL>ITKVEKGKVKEVATKLG

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	0.09 RPM	0.00 RPM
bodymap2_breast	0.14 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.04 RPM	0.00 RPM
bodymap2_kidney	0.10 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	0.04 RPM	0.00 RPM
bodymap2_prostate	0.00 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.16 RPM	0.00 RPM
bodymap2_testis	0.02 RPM	0.00 RPM
bodymap2_thyroid	0.09 RPM	0.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_218 was not detected

EST

No EST(s) were mapped for retro_hsap_218 retrocopy.

TSS

No TSS is located nearby retro_hsap_218 retrocopy 5' end.

Lab

retro_hsap_218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_218 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_288

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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	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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