RetrogeneDB ID: retro_hsap_3476

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:56894385..56894671(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: C2orf15
• Ensembl ID: ENSG00000241962
• Aliases: MRPL30, L28MT, L30MT, MRP-L28, MRP-L30, MRPL28, MRPL28M, RPML28
• Description: chromosome 2 open reading frame 15 [Source:HGNC Symbol;Acc:28436]

Sequence

>retro_hsap_3476
AGTCTCATTTGTACAGATTGGATTCGTCACAAATTCACCAGATCAAAAATTCCAGATAAAGTGTTTCACGCCTCACCTGA
AGATCATGAAAAATATGGTGGGGATCCACAGAACCCTCATAAACTGCATATTGTTACCAGAATAAAAAGTACAAAATACG
TCCATATTGGGAAAAAGATATAATAAAGAAGCTTGGATTGGAAAAATCACATATCCCTCAAGTTCACCAGAATTCCCTTC
AGTGAATGCAAAATTGAAAGTGGTTAAGCATTTGATAAGAATTGAA

Alignment

ORF - retro_hsap_3476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.73 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLICTDWIRHKFTRSRIPEKVFQASPEDHEKYGGDPQNPHKLHIVTRIKSTRR-RPYWEKDIIKMLGLEK
          SLICTDWIRHKFTRS.IP.KVF.ASPEDHEKYGGDPQNPHKLHIVTRIKST...RPYWEKDIIK.LGLEK
Retrocopy SLICTDWIRHKFTRSKIPDKVFHASPEDHEKYGGDPQNPHKLHIVTRIKSTKY<RPYWEKDIIKKLGLEK

Parental  AHTPQVHKN-IPSVNAKLKVVKHLIRIK
          .H.PQVH.N..PSVNAKLKVVKHLIRI.
Retrocopy SHIPQVHQN<FPSVNAKLKVVKHLIRIE

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	0.54 RPM
bodymap2_adrenal	0.00 RPM	2.23 RPM
bodymap2_brain	0.00 RPM	2.77 RPM
bodymap2_breast	0.00 RPM	2.10 RPM
bodymap2_colon	0.00 RPM	0.37 RPM
bodymap2_heart	0.00 RPM	0.31 RPM
bodymap2_kidney	0.00 RPM	6.25 RPM
bodymap2_liver	0.00 RPM	0.27 RPM
bodymap2_lung	0.00 RPM	0.65 RPM
bodymap2_lymph_node	0.09 RPM	2.19 RPM
bodymap2_ovary	0.00 RPM	1.91 RPM
bodymap2_prostate	0.16 RPM	1.92 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.18 RPM
bodymap2_testis	0.00 RPM	3.09 RPM
bodymap2_thyroid	0.00 RPM	3.37 RPM
bodymap2_white_blood_cells	0.16 RPM	1.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3476 was not detected

EST

No EST(s) were mapped for retro_hsap_3476 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_167017	1247 libraries	559 libraries	23 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_3476 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3476 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2356
Gorilla gorilla	retro_ggor_2343

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013344	1 retrocopy	retro_amel_1121,
Bos taurus	ENSBTAG00000038949	1 retrocopy	retro_btau_1542,
Canis familiaris	ENSCAFG00000031628	1 retrocopy	retro_cfam_1703,
Choloepus hoffmanni	ENSCHOG00000005804	2 retrocopies	retro_chof_2339, retro_chof_715,
Callithrix jacchus	ENSCJAG00000007085	1 retrocopy	retro_cjac_758,
Dasypus novemcinctus	ENSDNOG00000018648	5 retrocopies	retro_dnov_1430, retro_dnov_1469, retro_dnov_2019, retro_dnov_2348, retro_dnov_571,
Equus caballus	ENSECAG00000015993	1 retrocopy	retro_ecab_309,
Echinops telfairi	ENSETEG00000005006	4 retrocopies	retro_etel_168, retro_etel_2176, retro_etel_232, retro_etel_605,
Felis catus	ENSFCAG00000024233	4 retrocopies	retro_fcat_1430, retro_fcat_196, retro_fcat_528, retro_fcat_669,
Homo sapiens	ENSG00000241962	2 retrocopies	retro_hsap_3476 , retro_hsap_981,
Gorilla gorilla	ENSGGOG00000011677	2 retrocopies	retro_ggor_2343, retro_ggor_783,
Microcebus murinus	ENSMICG00000011627	4 retrocopies	retro_mmur_109, retro_mmur_1281, retro_mmur_61, retro_mmur_897,
Myotis lucifugus	ENSMLUG00000029851	2 retrocopies	retro_mluc_1543, retro_mluc_1786,
Mustela putorius furo	ENSMPUG00000011085	1 retrocopy	retro_mputfur_214,
Mus musculus	ENSMUSG00000026087	7 retrocopies	retro_mmus_1171, retro_mmus_1367, retro_mmus_1758, retro_mmus_331, retro_mmus_3680, retro_mmus_3724, retro_mmus_755,
Nomascus leucogenys	ENSNLEG00000026974	2 retrocopies	retro_nleu_2761, retro_nleu_337,
Oryctolagus cuniculus	ENSOCUG00000004111	1 retrocopy	retro_ocun_1946,
Otolemur garnettii	ENSOGAG00000002241	11 retrocopies	retro_ogar_1328, retro_ogar_1429, retro_ogar_2160, retro_ogar_2277, retro_ogar_2389, retro_ogar_3516, retro_ogar_401, retro_ogar_466, retro_ogar_549, retro_ogar_879, retro_ogar_908,
Ochotona princeps	ENSOPRG00000007331	2 retrocopies	retro_opri_826, retro_opri_989,
Pan troglodytes	ENSPTRG00000012275	2 retrocopies	retro_ptro_2356, retro_ptro_765,
Pteropus vampyrus	ENSPVAG00000006587	5 retrocopies	retro_pvam_1469, retro_pvam_1484, retro_pvam_321, retro_pvam_432, retro_pvam_764,
Rattus norvegicus	ENSRNOG00000018511	6 retrocopies	retro_rnor_2018, retro_rnor_2683, retro_rnor_2684, retro_rnor_2873, retro_rnor_570, retro_rnor_916,
Rattus norvegicus	ENSRNOG00000049330	1 retrocopy	retro_rnor_2976,
Sus scrofa	ENSSSCG00000008183	2 retrocopies	retro_sscr_529, retro_sscr_555,
Tarsius syrichta	ENSTSYG00000005345	4 retrocopies	retro_tsyr_1736, retro_tsyr_2153, retro_tsyr_368, retro_tsyr_866,
Tursiops truncatus	ENSTTRG00000004937	3 retrocopies	retro_ttru_1126, retro_ttru_1379, retro_ttru_78,