RetrogeneDB ID: retro_hsap_1111

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:46397935..46398266(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000239397
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSG00000142541
• Aliases: RPL13A, L13A, TSTA1
• Description: ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]

Sequence

>retro_hsap_1111
ACCCTACCACTTCTGGGTCTCTTCTACTTTCGGGCACCTAACTGCATCTTTTGGCTGAACCATGAGTGGTATATTGCCCC
ATAAAACCAAGTGAGGCCTGGCCACCTGGACCACCTCAAGGTATTTGATGGGATCCACACCCCCTGTGCCCTGCCCTTTG
CAAAAGTGGATGGTGATTTCTACTCTACTCAAGGTTGTGCACCTGAAGCCCACACTGAAGTTTGCCTACCTGGGGCACCT
GGTTCATAAATTTGCCTGGAAGTACCAACCAGTGACAGCCATTCTGGAGGAGAAGAGGAAGGAGAAGGTCAAGATCCATT
AGGAGAAAGAA

Alignment

ORF - retro_hsap_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.95 %
• Parental protein coverage: 53.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TNPSRGPYHFRAPSRIFWR-TVRGMLPHKTKRGQAALDRLKVFDGIPPPYD--KKKRMVVPAALKVVRLK
          T.P..G...FRAP..IFW..T..G.LPHKTK.G.A.........G..PP......K.MV....LKVV.LK
Retrocopy TLPLLGLFYFRAPNCIFWL>TMSGILPHKTK*GLATWTTSRYLMGSTPPVPCPLQKWMVISTLLKVVHLK

Parental  PTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKK
          PT.KFAYLG.L.H...WKYQ.VTA.LEEKRKEK.KIH..K.
Retrocopy PTLKFAYLGHLVHKFAWKYQPVTAILEEKRKEKVKIH*EKE

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	967.42 RPM
bodymap2_adrenal	0.00 RPM	1518.40 RPM
bodymap2_brain	0.00 RPM	156.35 RPM
bodymap2_breast	0.00 RPM	689.11 RPM
bodymap2_colon	0.00 RPM	1303.66 RPM
bodymap2_heart	0.00 RPM	269.24 RPM
bodymap2_kidney	0.00 RPM	446.76 RPM
bodymap2_liver	0.00 RPM	328.33 RPM
bodymap2_lung	0.00 RPM	1095.62 RPM
bodymap2_lymph_node	0.00 RPM	1494.82 RPM
bodymap2_ovary	0.00 RPM	1466.56 RPM
bodymap2_prostate	0.00 RPM	1422.20 RPM
bodymap2_skeletal_muscle	0.00 RPM	598.29 RPM
bodymap2_testis	0.09 RPM	649.24 RPM
bodymap2_thyroid	0.00 RPM	674.57 RPM
bodymap2_white_blood_cells	0.00 RPM	1717.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1111 was not detected

EST

No EST(s) were mapped for retro_hsap_1111 retrocopy.

TSS

No TSS is located nearby retro_hsap_1111 retrocopy 5' end.

Lab

retro_hsap_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1111 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_869

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris	ENSCAFG00000029892	3 retrocopies	retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Homo sapiens	ENSG00000142541	22 retrocopies	retro_hsap_1072, retro_hsap_1100, retro_hsap_1111 , retro_hsap_1268, retro_hsap_1410, retro_hsap_2200, retro_hsap_2500, retro_hsap_293, retro_hsap_298, retro_hsap_3173, retro_hsap_3350, retro_hsap_3444, retro_hsap_3652, retro_hsap_3752, retro_hsap_3772, retro_hsap_397, retro_hsap_436, retro_hsap_615, retro_hsap_671, retro_hsap_730, retro_hsap_753, retro_hsap_967,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,

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	0.04 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	0.03 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	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 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	0.03 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	0.05 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).