RetrogeneDB ID: retro_hsap_3024

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:13649703..13650024(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000242209
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSG00000144713
• Aliases: RPL32, L32
• Description: ribosomal protein L32 [Source:HGNC Symbol;Acc:10336]

Sequence

>retro_hsap_3024
ATGGCCACCTTCATACCCCTTGTGAAGCCCAAAATAGTCAAAAAGAGAACCAAGAAATTCATCGGGCACCGGTCAGACTG
ATATGTCAAAATTAAGCGTGACTGGCAGAAACCCAGAGGTAGTGACAACAGGGTTCATAGAAGGTTCAAGCTCCAGATCT
TGATGCCCAACATTACTTATGGGAGCAACAAAAAAACAAAGCATATGCTGCCCAGTGGCTTCCAGAAGTTCCTGGCCCAC
AAGGTCAAGGAGCAGGAAGTGCTGCTGATGTGCAACAAATCTTACTGTGCTGAGATTGCTCACAATGTTTCCTCCAACAA
C

Alignment

ORF - retro_hsap_3024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 79.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
          MA...PLVKPKIVKKRTKKFI.H.SD.YVKIKR.W.KPRG.DNRV.RRFK.QILMPNI.YGSNKKTKHML
Retrocopy MATFIPLVKPKIVKKRTKKFIGHRSD*YVKIKRDWQKPRGSDNRVHRRFKLQILMPNITYGSNKKTKHML

Parental  PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKN
          PSGF.KFL.H.VKE.EVLLMCNKSYCAEIAHNVSS.N
Retrocopy PSGFQKFLAHKVKEQEVLLMCNKSYCAEIAHNVSSNN

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	475.56 RPM
bodymap2_adrenal	0.00 RPM	645.14 RPM
bodymap2_brain	0.02 RPM	173.69 RPM
bodymap2_breast	0.00 RPM	411.62 RPM
bodymap2_colon	0.00 RPM	532.72 RPM
bodymap2_heart	0.00 RPM	193.31 RPM
bodymap2_kidney	0.00 RPM	252.38 RPM
bodymap2_liver	0.00 RPM	251.27 RPM
bodymap2_lung	0.00 RPM	695.97 RPM
bodymap2_lymph_node	0.00 RPM	911.91 RPM
bodymap2_ovary	0.00 RPM	690.71 RPM
bodymap2_prostate	0.00 RPM	978.90 RPM
bodymap2_skeletal_muscle	0.00 RPM	881.20 RPM
bodymap2_testis	0.00 RPM	384.92 RPM
bodymap2_thyroid	0.00 RPM	314.29 RPM
bodymap2_white_blood_cells	0.00 RPM	1080.68 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3024 was not detected

EST

No EST(s) were mapped for retro_hsap_3024 retrocopy.

TSS

No TSS is located nearby retro_hsap_3024 retrocopy 5' end.

Lab

retro_hsap_3024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3024 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 103 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Cavia porcellus	ENSCPOG00000019967	2 retrocopies	retro_cpor_1241, retro_cpor_608,
Dipodomys ordii	ENSDORG00000008426	6 retrocopies	retro_dord_175, retro_dord_251, retro_dord_371, retro_dord_458, retro_dord_522, retro_dord_664,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Erinaceus europaeus	ENSEEUG00000011609	5 retrocopies	retro_eeur_161, retro_eeur_247, retro_eeur_300, retro_eeur_39, retro_eeur_576,
Homo sapiens	ENSG00000144713	20 retrocopies	retro_hsap_1013, retro_hsap_1115, retro_hsap_1547, retro_hsap_1789, retro_hsap_1956, retro_hsap_2618, retro_hsap_2821, retro_hsap_2891, retro_hsap_3024 , retro_hsap_3450, retro_hsap_3536, retro_hsap_3582, retro_hsap_3726, retro_hsap_3805, retro_hsap_3936, retro_hsap_3982, retro_hsap_4008, retro_hsap_4155, retro_hsap_4677, retro_hsap_814,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Myotis lucifugus	ENSMLUG00000022528	6 retrocopies	retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Mus musculus	ENSMUSG00000057841	16 retrocopies	retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099, retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Ictidomys tridecemlineatus	ENSSTOG00000026505	9 retrocopies	retro_itri_1294, retro_itri_1322, retro_itri_1465, retro_itri_1639, retro_itri_1715, retro_itri_1748, retro_itri_370, retro_itri_885, retro_itri_948,