RetrogeneDB ID: retro_hsap_2172

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:159404936..159405733(+)
• Located in intron of: ENSG00000144283

Retrocopy information

• Ensembl ID: ENSG00000227331
• 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_2172
ATGCCAAAAGGAAAGAAGGCCAAGGGGAAGAAGGTGGCCCTGGCCCCTGTTGTTGCAGAGAAGCAGGAGGCCAAGAAAGT
GATGGATCCCCTGTTTGAGAAAAGACCTGAGAATTTTGGCATTGGATAGGACATCTAGCCCAAATGGGATCTTAACCCAC
TTTGTCAAATGCCCCTGCTACTACATCAGGTTGCAGCAGCAAAGAGCTGTCCTCTATCCAGAGCTGAAAGTGCCTCTTGC
GATGAACCAGTTCACCCCGGCCGTGGACCGCCAAGCAGCTACTCAGCTGCTTAAGCTGGCCCATAAGTACTGACCAGAGA
CAAAGCAAGAGAAGAAGCAGAGACTTGGCCTGGGCTGAGAAGAAAGCTGCCAGCAAAGGGAACATCCCCATTAAGAGACC
ACCTGTCCTTCGAGTAGGGGTTAACATTGTCACCACCTTTGGAGAACAAGAAGGCTCAGCTGGTGGTGATCGCACATGAC
ATGGATCCCATTGAGCCAGTTGTCTTCCTGCTTGCCTTATGTCCTAAAATGGGGGTCCTTGACTGCATTATCAAGGGGAA
GGCAAGCCTGGGATGTCTGTGCATAGGAAGACCCTGCACCACTGTTGCCTTCACACAGGTTAACTTGGAAGACAAAGGAG
CTTCGGTTAGCTGGTGGAAACTATCAGGACCAATTACAATGATAGATATGATGAGATCCGCCATCACTGGGGAGGCAGTG
TCCTGGGTTCCAAGTCTGTGGCTTGCTTTGCCAAGCTGGAAAGGGCAAACGCTAAAGGACTTGCCACTAAACTGGGT

Alignment

ORF - retro_hsap_2172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDL-TRFVKWP-RYIRLQRQRA
          MPKGKKAKGKKVA.AP.V..KQEAKKV..PLFEKRP.NFGIG.DI.PK.DL.T.FVK.P..YIRLQ.QRA
Retrocopy MPKGKKAKGKKVALAPVVAEKQEAKKVMDPLFEKRPENFGIG*DI*PKWDL>THFVKCPCYYIRLQQQRA

Parental  ILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK-KAAGKGDVP-TKRPPVL
          .LY..LKVP.A.NQFT.A.DRQ.ATQLLKLAHKY.PETKQEKKQRL....E..K...KG..P..KRPPVL
Retrocopy VLYPELKVPLAMNQFTPAVDRQAATQLLKLAHKY*PETKQEKKQRLGLG*EE<KLPAKGTSP<IKRPPVL

Parental  RAGVNTVTT-LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRL-VHRKT-CTTVA
          R.GVN.VTT.L...K....V..AHD.DPIE.VVFL.ALC.KMGV..CIIKGKA.LG.L.VHRKT.CTTVA
Retrocopy RVGVNIVTT>LENKKAQLVVI-AHDMDPIEPVVFLLALCPKMGVLDCIIKGKASLGCL<VHRKT>CTTVA

Parental  FTQVNSEDKGALAK-LVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG
          FTQVN.EDKGA....LVE.IRTNYNDRYDEIR.HWGG.VLG.KSVA..AKLE.A.AK.LATKLG
Retrocopy FTQVNLEDKGASVS<LVETIRTNYNDRYDEIRHHWGGSVLGSKSVACFAKLERANAKGLATKLG

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	0.14 RPM	0.00 RPM
bodymap2_brain	0.00 RPM	0.00 RPM
bodymap2_breast	0.31 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.06 RPM	0.00 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.11 RPM	0.00 RPM
bodymap2_lymph_node	0.20 RPM	0.00 RPM
bodymap2_ovary	0.02 RPM	0.00 RPM
bodymap2_prostate	0.10 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.00 RPM	0.00 RPM
bodymap2_thyroid	0.06 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_2172 was not detected

EST

No EST(s) were mapped for retro_hsap_2172 retrocopy.

TSS

No TSS is located nearby retro_hsap_2172 retrocopy 5' end.

Lab

retro_hsap_2172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2172 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1724

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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,