RetrogeneDB ID: retro_hsap_1263

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:48340896..48341231(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000229423
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSG00000166441
• Aliases: RPL27A, L27A
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_hsap_1263
ATACCATTCAGGCTGAGGAAGACCCAGAAACTTCTGGGCCATGTAAGCCACAGCCACAGCCTCATCAGCAAGCACCAAAA
GCACTCCGGAGGCAGGAGTAATACTGGTGGCAAGCATCACCACAGGATCAACTTTGACAAACCTCACCTAGGTTCCTTTG
GGAAAGTTGGTATAAGGGTTACCACTTAAAGAGGAACCAGAGCTCCTGCTCAAATGCCAACCCTGATAAATTGTGGACTT
TGGTCAGTGTACAGACACAGGTGAATGCTGCTAAAGACAAAACTGGAGCTGCTCCCACCATTGATGTGGTGTGATCAGGC
TACTACAAAGTTCTG

Alignment

ORF - retro_hsap_1263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 75.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGM-KHYHLKRNQSF
          .P.RLRKT.KL.GHVSH.H..I.KH.KH.GGR.N.GG.HHHRINFDK.H.G.FGKVG..K.YHLKRNQS.
Retrocopy IPFRLRKTQKLLGHVSHSHSLISKHQKHSGGRSNTGGKHHHRINFDKPHLGSFGKVGI<KGYHLKRNQSS

Parental  CPTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVL
          C...N.DKLWTLVS.QT.VNAAK.KTGAAP.IDVV.SGYYKVL
Retrocopy CSNANPDKLWTLVSVQTQVNAAKDKTGAAPTIDVV*SGYYKVL

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	407.04 RPM
bodymap2_adrenal	0.00 RPM	683.19 RPM
bodymap2_brain	0.00 RPM	103.14 RPM
bodymap2_breast	0.00 RPM	309.93 RPM
bodymap2_colon	0.00 RPM	485.08 RPM
bodymap2_heart	0.00 RPM	123.73 RPM
bodymap2_kidney	0.00 RPM	179.49 RPM
bodymap2_liver	0.00 RPM	187.33 RPM
bodymap2_lung	0.00 RPM	563.40 RPM
bodymap2_lymph_node	0.00 RPM	575.42 RPM
bodymap2_ovary	0.00 RPM	534.80 RPM
bodymap2_prostate	0.00 RPM	586.75 RPM
bodymap2_skeletal_muscle	0.00 RPM	291.64 RPM
bodymap2_testis	0.00 RPM	232.16 RPM
bodymap2_thyroid	0.00 RPM	324.56 RPM
bodymap2_white_blood_cells	0.00 RPM	719.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1263 was not detected

EST

No EST(s) were mapped for retro_hsap_1263 retrocopy.

TSS

No TSS is located nearby retro_hsap_1263 retrocopy 5' end.

Lab

retro_hsap_1263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166441	7 retrocopies	retro_hsap_1263 , retro_hsap_1908, retro_hsap_2352, retro_hsap_239, retro_hsap_3335, retro_hsap_3586, retro_hsap_3682,
Gorilla gorilla	ENSGGOG00000001660	2 retrocopies	retro_ggor_155, retro_ggor_1785,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta	ENSMMUG00000021828	2 retrocopies	retro_mmul_207, retro_mmul_268,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Pan troglodytes	ENSPTRG00000003333	1 retrocopy	retro_ptro_33,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Tarsius syrichta	ENSTSYG00000013207	16 retrocopies	retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 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	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 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	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 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	0.00 RPM

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Indel association:

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