RetrogeneDB ID: retro_ptro_1947

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:174491585..174491904(-)
• Located in intron of: ENSPTRG00000015617

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL28
• Ensembl ID: ENSPTRG00000011505
• Aliases: None
• Description: ribosomal protein L28 [Source:HGNC Symbol;Acc:10330]

Sequence

>retro_ptro_1947
ATGTCTGCGCATCTGCAATCGGTGATCATGCGAAACTGCTCCAGTTTCCTGATCAAGAGGAATAAACACACCTACAGCAC
CGAGCCCAATAACTTGAAGGCCCGCAACTCCTTCCCGCTACAACCGGCTGATTCACTGCAAGACTGTGGGCGTGGAGCCG
GCAGCCCATGGCAGAGGTGTCCTGGTGGTCATGAAGCGGAGATCCGGCCAGCGGACGCCTGCCATCTCCTACGTGCGGAC
CATCATCAACAAGAACGCTGGAGCCAAACTCAGCAGCATCAGATACATGATCCGCAAGAACAAGTACCGCCCTGACCTG

Alignment

ORF - retro_ptro_1947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 62.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSF-RYNGLIHRKTVGVEPAADGKGVVVVIKRRSG
          MSAHLQ....RNCSSFLIKRNK.TYSTEPNNLKARNSF.RYN.LIH.KTVGVEPAA.G.GV.VV.KRRSG
Retrocopy MSAHLQSVIMRNCSSFLIKRNKHTYSTEPNNLKARNSF>RYNRLIHCKTVGVEPAAHGRGVLVVMKRRSG

Parental  QRKPATSYVRTTINKNARATLSSIRHMIRKNKYRPDL
          QR.PA.SYVRT.INKNA.A.LSSIR.MIRKNKYRPDL
Retrocopy QRTPAISYVRTIINKNAGAKLSSIRYMIRKNKYRPDL

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
SRP007412_brain_prefrontal_cortex	0.05 RPM	91.95 RPM
SRP007412_cerebellum	0.00 RPM	18.61 RPM
SRP007412_heart	0.00 RPM	18.45 RPM
SRP007412_kidney	0.00 RPM	76.78 RPM
SRP007412_liver	0.00 RPM	30.74 RPM
SRP007412_testis	0.00 RPM	6.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1947 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1947 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2879
Gorilla gorilla	retro_ggor_1995
Pongo abelii	retro_pabe_2383

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015980	1 retrocopy	retro_acar_10,
Ailuropoda melanoleuca	ENSAMEG00000003764	15 retrocopies	retro_amel_1006, retro_amel_1099, retro_amel_1155, retro_amel_1369, retro_amel_1393, retro_amel_1465, retro_amel_1737, retro_amel_231, retro_amel_289, retro_amel_33, retro_amel_474, retro_amel_556, retro_amel_630, retro_amel_822, retro_amel_829,
Callithrix jacchus	ENSCJAG00000000869	1 retrocopy	retro_cjac_218,
Cavia porcellus	ENSCPOG00000012833	2 retrocopies	retro_cpor_127, retro_cpor_214,
Dipodomys ordii	ENSDORG00000012809	2 retrocopies	retro_dord_242, retro_dord_789,
Equus caballus	ENSECAG00000026938	2 retrocopies	retro_ecab_1020, retro_ecab_721,
Felis catus	ENSFCAG00000005639	15 retrocopies	retro_fcat_1045, retro_fcat_1214, retro_fcat_1397, retro_fcat_1404, retro_fcat_1463, retro_fcat_1629, retro_fcat_1663, retro_fcat_171, retro_fcat_233, retro_fcat_484, retro_fcat_575, retro_fcat_786, retro_fcat_904, retro_fcat_910, retro_fcat_942,
Homo sapiens	ENSG00000108107	4 retrocopies	retro_hsap_1503, retro_hsap_1964, retro_hsap_2879, retro_hsap_3380,
Gorilla gorilla	ENSGGOG00000022653	4 retrocopies	retro_ggor_1154, retro_ggor_1427, retro_ggor_1995, retro_ggor_2288,
Macropus eugenii	ENSMEUG00000015744	1 retrocopy	retro_meug_1497,
Myotis lucifugus	ENSMLUG00000023789	1 retrocopy	retro_mluc_325,
Macaca mulatta	ENSMMUG00000015901	1 retrocopy	retro_mmul_68,
Monodelphis domestica	ENSMODG00000000275	1 retrocopy	retro_mdom_1458,
Mus musculus	ENSMUSG00000030432	10 retrocopies	retro_mmus_162, retro_mmus_1679, retro_mmus_1911, retro_mmus_2511, retro_mmus_2526, retro_mmus_2606, retro_mmus_2629, retro_mmus_3149, retro_mmus_362, retro_mmus_738,
Nomascus leucogenys	ENSNLEG00000010503	4 retrocopies	retro_nleu_1287, retro_nleu_2607, retro_nleu_619, retro_nleu_969,
Otolemur garnettii	ENSOGAG00000025533	4 retrocopies	retro_ogar_2078, retro_ogar_788, retro_ogar_809, retro_ogar_892,
Petromyzon marinus	ENSPMAG00000008617	1 retrocopy	retro_pmar_10,
Pongo abelii	ENSPPYG00000010417	4 retrocopies	retro_pabe_1691, retro_pabe_1869, retro_pabe_2383, retro_pabe_2778,
Pan troglodytes	ENSPTRG00000011505	4 retrocopies	retro_ptro_1312, retro_ptro_1947 , retro_ptro_2297, retro_ptro_3181,
Rattus norvegicus	ENSRNOG00000017127	5 retrocopies	retro_rnor_1588, retro_rnor_2117, retro_rnor_243, retro_rnor_610, retro_rnor_855,
Ictidomys tridecemlineatus	ENSSTOG00000008006	1 retrocopy	retro_itri_656,
Tursiops truncatus	ENSTTRG00000002428	5 retrocopies	retro_ttru_1246, retro_ttru_1464, retro_ttru_1668, retro_ttru_696, retro_ttru_936,