RetrogeneDB ID: retro_hsap_1553

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:40604864..40605490(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000244705
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSG00000089157
• Aliases: RPLP0, L10E, LP0, P0, PRLP0, RPP0
• Description: ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]

Sequence

>retro_hsap_1553
ATGCCCAGGGAAGACAGGATGACCTGGAAGTCCAACTACTTCAAGATCATCCAGCTTTTGGATGATTATCCAAAATGTTT
CATCGTGGGAGCAGCAATGTGGGCTCCAAGCAGACGCAGCAGATCTGCATGTCCCTCTGAGAGAAGGCCGTGGTGCTGAT
GGACAAGAACACCATGATGCTCACGGCCATCTGAGGGCACCTGGAAAACAACCCAGCTCTGGAGAAACTGCTGCCTCATA
TCTGGGGGAATGTGGGCTTTGCATTCACCAAGGAGGACCTCACTGAAATCAAGGACATGTTGCTGGCTAGTAAGGTGCCA
GCTGCCACCTGTGCTGGTCCCATTGCCCCATGTGAAGTCACTGTGCCAGCCCAGAACACTGGTCTGGGGCCAGAGAAAAC
CTCCTTTTTCCAGGCTTTAGGAATCACCACTAAAATCTCCAGGGGCACCATTGAAATCCTGAGTGATGTGCAGCTGATCA
AGACTGGAGACAAAGTGGGAGCCAACAAAGCCACGCTGCTGAACACGCCGAGCATTTCTCCCTCCTCCTTTGCGCTGGTC
ATCCAGCAGGCATCTGACAATGGCAGCATCTACAACCCTGAAGTGCTTGACATCACAGAGGAAACT

Alignment

ORF - retro_hsap_1553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.73 %
• Parental protein coverage: 66.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPREDRATWKSNYFLKIIQLLDDYPKCFIVGA-DNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHL
          MPREDR.TWKSNYF.KIIQLLDDYPKCFIVGA..NVGSKQ.QQI.MSL..KAVVLM.KNTMM..AI.GHL
Retrocopy MPREDRMTWKSNYF-KIIQLLDDYPKCFIVGA<SNVGSKQTQQICMSL*EKAVVLMDKNTMMLTAI*GHL

Parental  ENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQ
          ENNPALEKLLPHI.GNVGF.FTKEDLTEI.DMLLA.KVPAA..AG.IAPCEVTVPAQNTGLGPEKTSFFQ
Retrocopy ENNPALEKLLPHIWGNVGFAFTKEDLTEIKDMLLASKVPAATCAGPIAPCEVTVPAQNTGLGPEKTSFFQ

Parental  ALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEE
          ALGITTKISRGTIEILSDVQLIKTGDKVGA..ATLLN...ISP.SF.LVIQQ..DNGSIYNPEVLDITEE
Retrocopy ALGITTKISRGTIEILSDVQLIKTGDKVGANKATLLNTPSISPSSFALVIQQASDNGSIYNPEVLDITEE

Parental  T
          T
Retrocopy T

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	635.70 RPM
bodymap2_adrenal	0.00 RPM	730.78 RPM
bodymap2_brain	0.00 RPM	82.65 RPM
bodymap2_breast	0.00 RPM	427.83 RPM
bodymap2_colon	0.00 RPM	773.41 RPM
bodymap2_heart	0.00 RPM	202.81 RPM
bodymap2_kidney	0.00 RPM	471.29 RPM
bodymap2_liver	0.00 RPM	442.56 RPM
bodymap2_lung	0.00 RPM	667.16 RPM
bodymap2_lymph_node	0.00 RPM	1096.55 RPM
bodymap2_ovary	0.02 RPM	707.90 RPM
bodymap2_prostate	0.00 RPM	1087.79 RPM
bodymap2_skeletal_muscle	0.00 RPM	558.44 RPM
bodymap2_testis	0.09 RPM	383.53 RPM
bodymap2_thyroid	0.00 RPM	482.21 RPM
bodymap2_white_blood_cells	0.00 RPM	841.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1553 was not detected

EST

No EST(s) were mapped for retro_hsap_1553 retrocopy.

TSS

No TSS is located nearby retro_hsap_1553 retrocopy 5' end.

Lab

retro_hsap_1553 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1553 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005144	4 retrocopies	retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris	ENSCAFG00000010227	5 retrocopies	retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus	ENSECAG00000015816	2 retrocopies	retro_ecab_1090, retro_ecab_585,
Felis catus	ENSFCAG00000013354	1 retrocopy	retro_fcat_441,
Homo sapiens	ENSG00000089157	7 retrocopies	retro_hsap_1403, retro_hsap_1553 , retro_hsap_1889, retro_hsap_2095, retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Myotis lucifugus	ENSMLUG00000001970	11 retrocopies	retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis	ENSPCAG00000016429	6 retrocopies	retro_pcap_232, retro_pcap_314, retro_pcap_339, retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Tursiops truncatus	ENSTTRG00000005658	1 retrocopy	retro_ttru_965,